From m.reynaud at obbec.com Mon Apr 3 09:48:18 2006 From: m.reynaud at obbec.com (Marie Reynaud) Date: Mon, 03 Apr 2006 15:48:18 +0200 Subject: [BiO BB] Bioinformatics, Fresh Data, New Approach Message-ID: <443127A2.7020107@obbec.com> Dear Sir or Madam, *JOIN US NOW.* Subscribe online for *FREE** to the world's most exclusive *Life Science computing and technology* magazine! Produced to meet the needs of healthcare and information technology professionals, executives, decision makers, senior scientists and researchers in the life science sectors, *OBBeC?* is an authoritative international business-to-business magazine with a global focus on the developments in life sciences and healthcare, influenced by the latest advances in computing and IT technologies. *OBBeC? 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Marie Reynaud International Marketing Director OBBeC? Media Publications www.obbec.com *February 2006 issue * OBBeC? Magazine Demo *Click to View Demo* *(First 20 Pages Only)* PPA Member of Periodical Publishers Association _* Editorial Associates:*_ Frost & Sullivan EMBL-EBI *CONFIDENTIALITY NOTICE* This e-mail contains information which is confidential and privileged. If you are not the intended recipient please note that any copying, use, dissemination or taking any action in reliance on the contents of this email is prohibited and unlawful. If you have received this email in error, please delete the message and notify the sender immediately by replying to this e-mail. This e-mail and attachments have been scanned for viruses prior to sending. OBBeC? Media Publications will not be liable for any losses as a result of any viruses being passed on. *offer for a limited period only. From jeff at bioinformatics.org Mon Apr 3 10:31:43 2006 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Mon, 03 Apr 2006 10:31:43 -0400 Subject: [BiO BB] Bioinformatics, Fresh Data, New Approach In-Reply-To: <443127A2.7020107@obbec.com> References: <443127A2.7020107@obbec.com> Message-ID: <443131CF.5070408@bioinformatics.org> Our apologies for the unsolicited product announcement getting through. Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From bioinfosm at gmail.com Mon Apr 3 13:13:25 2006 From: bioinfosm at gmail.com (Samantha Fox) Date: Mon, 3 Apr 2006 13:13:25 -0400 Subject: [BiO BB] KEGG vs GO Message-ID: <726450810604031013m3cd2d0eas87ac724bf308067a@mail.gmail.com> Hi there, I was wondering how KEGG and GO differ from a broad perspective of grouping functionally related genes. So a KEGG pathway lists all genes that kind of work together, and a similar GO term would also contain such a gene list. Has anyone used KEGG and GO to that detail to explain this ! Thanks, ~S -------------- next part -------------- An HTML attachment was scrubbed... URL: From lucifer at slimy.greenend.org.uk Tue Apr 4 12:46:43 2006 From: lucifer at slimy.greenend.org.uk (lucifer at slimy.greenend.org.uk) Date: Tue, 04 Apr 2006 17:46:43 +0100 Subject: [BiO BB] KEGG vs GO In-Reply-To: <20060404160115.63BD39404F@primary.bioinformatics.org> References: <20060404160115.63BD39404F@primary.bioinformatics.org> Message-ID: "Samantha Fox" writes: > I was wondering how KEGG and GO differ from a broad perspective of > grouping functionally related genes. So a KEGG pathway lists all genes > that kind of work together, and a similar GO term would also contain such > a gene list. IIRC, KEGG is manually created from the literature whilst GO also contains automatic/electronic annotation based on sequence homology. KEGG also focuses more on metabolic pathways, whilst GO covers a more comprehensive set of cellular processes and molecular functions. Hope that helps, Lucy -- Lucy McWilliam http://www.chiark.greenend.org.uk/~lucifer/ From oliviero.carugo at univie.ac.at Wed Apr 5 02:49:02 2006 From: oliviero.carugo at univie.ac.at (Oliviero Carugo) Date: Wed, 5 Apr 2006 08:49:02 +0200 (CEST) Subject: [BiO BB] WORKSHOP: PROTEIN DOMAINS - CRYSTALLIZATION Message-ID: <1123.131.130.79.98.1144219742.squirrel@webmail.univie.ac.at> ================================================== WORKSHOP ON THE DEFINITION OF PROTEIN DOMAINS AND THEIR LIKELIHOOD OF CRYSTALLIZATION University of Vienna 28th - 30th June 2006 ================================================== The workshop will cover experimental and computational techniques for identifying the boundaries of structural domains in proteins. Sessions will include: - In silico et in solido- new ideas and strategies to predict the likelihood of crystallization - Experimental identification of domain boundaries - Conformation disorder and compactness - Post-translational modification- state of the art in predicting coded modifications - Predictions of domain boundaries As well as talks by invited speakers, short talks will selected by the organizers from the submitted abstracts. For more information and in order to register see www.embl-hamburg.de/workshops/2006/domains/ The workshop is organized by the Department of Biomolecular Structural Chemistry (University of Vienna) in its capacity as a Training and Dissemination Centre for the EU 6th Framework VIZIER Integrated Project. ============================================= Oliviero Carugo Department of Biomolecular Structural Chemistry University of Vienna Campus-Vienna -Biocenter 5 1030 Vienna (Austria) Phone: +43-(0)1-4277-52208 Fax: +43-(0)1-4277-9522 Email: oliviero.carugo at univie.ac.at From dmb at mrc-dunn.cam.ac.uk Wed Apr 5 06:13:14 2006 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Wed, 05 Apr 2006 11:13:14 +0100 Subject: [BiO BB] KEGG vs GO In-Reply-To: References: <20060404160115.63BD39404F@primary.bioinformatics.org> Message-ID: <4433983A.1020304@mrc-dunn.cam.ac.uk> lucifer at slimy.greenend.org.uk wrote: > "Samantha Fox" writes: > >> I was wondering how KEGG and GO differ from a broad perspective of >> grouping functionally related genes. So a KEGG pathway lists all >> genes that kind of work together, and a similar GO term would also >> contain such > a gene list. > > > IIRC, KEGG is manually created from the literature whilst GO also > contains automatic/electronic annotation based on sequence homology. > KEGG also focuses more on metabolic pathways, whilst GO covers a more > comprehensive set of cellular processes and molecular functions. > > Hope that helps, It should be possible to 'cross correlate' KEGG an GO in a number of different ways using one of the SWISSPROT relational databases. However you should know that generally 'ontology mapping' is an open problem :) Good luck! > Lucy > -- > Lucy McWilliam > http://www.chiark.greenend.org.uk/~lucifer/ > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From ma11 at gen.cam.ac.uk Thu Apr 6 12:45:51 2006 From: ma11 at gen.cam.ac.uk (Michael Ashburner (Genetics)) Date: Thu, 6 Apr 2006 17:45:51 +0100 (BST) Subject: [BiO BB] KEGG vs GO Message-ID: I think that there is some confusion in this thread. 1. There is the Gene Ontology. Its terms are used (primarily) for the annotation of gene products. Both the Ontology and the annotations contributed by the members of the GO Consortium database are available from the GO site. 2. There is the KEGG Orthology, available from the KEGG site. This is _both_ an ontology, seen, for example, by opening KO up to its 3rd level: http://www.genome.ad.jp/dbget-bin/get_htext?KO+-s+F+-f+F+C _and_ annotations of classes of gene product, seen if it is opened up to level 4: http://www.genome.ad.jp/dbget-bin/get_htext?KO+-s+F+-f+F+D It would be easy for us to make a mapping between the Gene Ontology and KO (level 3), except that the KO includes domains outwith the GO (e.g. 01500 Human Diseases, and its child terms). In fact we will do that and make it available as a ko2go mapping file on GO. We do not need the "SwissProt Relational Database" to do this. Indeed, KEGG already provide many of these mappings to the GO. Mapping to level 4 is more problematic. The KO presents three levels: Ontology terms ("Levels 1-3") e.g.: 00010 Glycolysis / Gluconeogenesis PATH:ko00010] [GO:0006096 0006094] Families of proteins ("Level 4") e.g. K00845 E2.7.1.2, glk; glucokinase [EC:2.7.1.2] [COG:COG0837] [GO:0004340] Genes, whose products are members of this family e.g. Genes HSA: 2645(GCK) While for those Level 4 terms that are enzymes a 'mapping' of KO to the GO would not be hard, it gets more difficult further down. Consider the term: K06051 DLL; delta This is a child of (among others) Notch signaling pathway [PATH:ko04330] {which would map to the GO) and has children: HSA: 10683(DLL3) 28514(DLL1) 54567(DLL4) MMU: 13388(Dll1) 13389(Dll3) 54485(Dll4) RNO: 114125(Dll3) 311332(Dll4_predicted) 84010(Dll1) XLA: 379238(MGC52561) DRE: 30120(dlc) 30131(dla) 30138(dld) 30141(dlb) DME: CG3619-PA(Dmel_CG3619) Which are clearly individual gene products. Thus, I conclude, that KO's: K06051 DLL; delta is a _genus_ of gene products. This is conceptually very different from the GO, despite what may seem to be superficial similarities. So, contra Lucy, the difference between the GO and KO has nothing to do with manual vs automatic annotation, or on the 'focus' of the KO, but rather they differ in their underlying structure. Michael ===== Envelope-to: ma11 at gen.cam.ac.uk Delivery-date: Wed, 05 Apr 2006 11:14:38 +0100 X-Cam-SpamDetails: scanned, SpamAssassin (score=0) X-Cam-AntiVirus: No virus found X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Original-To: bio_bulletin_board at bioinformatics.org Delivered-To: bio_bulletin_board at bioinformatics.org X-Cam-SpamDetails: Not scanned X-Cam-AntiVirus: No virus found Date: Wed, 05 Apr 2006 11:13:14 +0100 From: Dan Bolser User-Agent: Mozilla Thunderbird 1.0.7-1.1.fc4 (X11/20050929) X-Accept-Language: en-us, en MIME-Version: 1.0 To: "The general forum at Bioinformatics.Org" Subject: Re: [BiO BB] KEGG vs GO Content-Transfer-Encoding: 7bit X-BeenThere: bio_bulletin_board at bioinformatics.org X-Mailman-Version: 2.1.5 List-Id: "The general forum at Bioinformatics.Org" List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-Keywords: lucifer at slimy.greenend.org.uk wrote: > "Samantha Fox" writes: > >> I was wondering how KEGG and GO differ from a broad perspective of >> grouping functionally related genes. So a KEGG pathway lists all >> genes that kind of work together, and a similar GO term would also >> contain such > a gene list. > > > IIRC, KEGG is manually created from the literature whilst GO also > contains automatic/electronic annotation based on sequence homology. > KEGG also focuses more on metabolic pathways, whilst GO covers a more > comprehensive set of cellular processes and molecular functions. > > Hope that helps, It should be possible to 'cross correlate' KEGG an GO in a number of different ways using one of the SWISSPROT relational databases. However you should know that generally 'ontology mapping' is an open problem :) Good luck! > Lucy > -- > Lucy McWilliam > http://www.chiark.greenend.org.uk/~lucifer/ > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From bioinfosm at gmail.com Thu Apr 6 14:54:25 2006 From: bioinfosm at gmail.com (Samantha Fox) Date: Thu, 6 Apr 2006 14:54:25 -0400 Subject: [BiO BB] KEGG vs GO In-Reply-To: References: Message-ID: <726450810604061154i24d4f26asc12e1f21beb7e30a@mail.gmail.com> Thanks all for the replies. It was nice reading Michael's explanation. So in effect if I am using sets of genes belonging to a particular pathway in 3rd level of KO, its quite similar to using the sets of genes sharing GO terms (just going by nomeclature for now, but we may later have ko2go mapping) ~S On 4/6/06, Michael Ashburner (Genetics) wrote: > > I think that there is some confusion in this thread. > > 1. There is the Gene Ontology. Its terms are used (primarily) > for the annotation of gene products. Both the Ontology and the > annotations contributed by the members of the GO Consortium database > are available from the GO site. > > 2. There is the KEGG Orthology, available from the KEGG site. > This is _both_ an ontology, seen, for example, by > opening KO up to its 3rd level: > http://www.genome.ad.jp/dbget-bin/get_htext?KO+-s+F+-f+F+C > _and_ annotations of classes of gene product, seen if it is opened up > to level 4: > http://www.genome.ad.jp/dbget-bin/get_htext?KO+-s+F+-f+F+D > > > It would be easy for us to make a mapping between the Gene Ontology > and KO (level 3), except that the KO includes domains outwith the GO > (e.g. 01500 Human Diseases, and its child terms). In fact we will > do that and make it available as a ko2go mapping file on GO. We do not > need the "SwissProt Relational Database" to do this. Indeed, KEGG already > provide many of these mappings to the GO. > > Mapping to level 4 is more problematic. The KO presents three levels: > > Ontology terms ("Levels 1-3") > e.g.: 00010 Glycolysis / Gluconeogenesis PATH:ko00010] [GO:0006096 > 0006094] > Families of proteins ("Level 4") > e.g. K00845 E2.7.1.2, glk; glucokinase [EC:2.7.1.2] [COG:COG0837] > [GO:0004340] > Genes, whose products are members of this family > e.g. Genes HSA: 2645(GCK) > > While for those Level 4 terms that are enzymes a 'mapping' of KO to the GO > would not be hard, it gets more difficult further down. Consider the > term: > K06051 DLL; delta > This is a child of (among others) > Notch signaling pathway [PATH:ko04330] {which would map to the GO) > and has children: > HSA: 10683(DLL3) 28514(DLL1) 54567(DLL4) > MMU: 13388(Dll1) 13389(Dll3) 54485(Dll4) > RNO: 114125(Dll3) 311332(Dll4_predicted) 84010(Dll1) > XLA: 379238(MGC52561) > DRE: 30120(dlc) 30131(dla) 30138(dld) 30141(dlb) > DME: CG3619-PA(Dmel_CG3619) > Which are clearly individual gene products. > > Thus, I conclude, that KO's: K06051 DLL; delta is a _genus_ > of gene products. This is conceptually very different from the GO, > despite what may seem to be superficial similarities. > > So, contra Lucy, the difference between the GO and KO has nothing to > do with manual vs automatic annotation, or on the 'focus' of the KO, > but rather they differ in their underlying structure. > > Michael > > > lucifer at slimy.greenend.org.uk wrote: > > "Samantha Fox" writes: > > > >> I was wondering how KEGG and GO differ from a broad perspective of > >> grouping functionally related genes. So a KEGG pathway lists all > >> genes that kind of work together, and a similar GO term would also > >> contain such > a gene list. > > > > > > IIRC, KEGG is manually created from the literature whilst GO also > > contains automatic/electronic annotation based on sequence homology. > > KEGG also focuses more on metabolic pathways, whilst GO covers a more > > comprehensive set of cellular processes and molecular functions. > > > > Hope that helps, > > It should be possible to 'cross correlate' KEGG an GO in a number of > different ways using one of the SWISSPROT relational databases. However > you should know that generally 'ontology mapping' is an open problem :) > > Good luck! -------------- next part -------------- An HTML attachment was scrubbed... URL: From janderson_net at yahoo.com Thu Apr 6 23:10:24 2006 From: janderson_net at yahoo.com (James Anderson) Date: Thu, 6 Apr 2006 20:10:24 -0700 (PDT) Subject: [BiO BB] question on processing LC/MS data Message-ID: <20060407031024.34859.qmail@web34009.mail.mud.yahoo.com> Hi, I am now working on some LC/MS data (the machine is made by Waters). I have the raw data file, each sample has very large size (in the order of several G bytes). Each file has 3 functions and each function has a lot of scans with each scan corresponding to a retention time. I have 6 control samples and 6 dosed samples, the purpose is to find those proteins that are differentially expressed between the two groups (control and dose). The data is the raw txt file produced by Water Q Tof. However, I don't know how to convert those txt files to NetCDF or mzXML format which could be processed by some software. In addition, the format of each sample is as follows: Each sample has 3 functions. Function 1. Full scan data Function 2. Cell collision voltage data, this is developed by Waters to identify peptides. Function 3. Lock mass data, which is used to calibrate the spectrum. Does anybody have similar experience processing this kind of data? Many thanks. James --------------------------------- New Yahoo! Messenger with Voice. Call regular phones from your PC and save big. -------------- next part -------------- An HTML attachment was scrubbed... URL: From safee.ullah at gmail.com Fri Apr 7 01:00:22 2006 From: safee.ullah at gmail.com (Safee) Date: Fri, 7 Apr 2006 14:00:22 +0900 Subject: [BiO BB] question on processing LC/MS data In-Reply-To: <20060407031024.34859.qmail@web34009.mail.mud.yahoo.com> References: <20060407031024.34859.qmail@web34009.mail.mud.yahoo.com> Message-ID: <624273170604062200o2a769efcm52938991119c7566@mail.gmail.com> Hi James, The Sashimi website at http://sashimi.sourceforge.net/ offers a collection of converter programs for some common mass spectrometer file formats. Try to find Waters QTOF in that list.. Regards safee ullah On 4/7/06, James Anderson wrote: > > Hi, > > I am now working on some LC/MS data (the machine is made by > > Waters). I have the raw data file, each sample has very large size (in the order > > of several G bytes). Each file has 3 functions and each function has a lot > > of scans with each scan corresponding to a retention time. I have 6 > > control samples and 6 dosed samples, the purpose is to find those proteins that > > are differentially expressed between the two groups (control and dose). > The data is the raw txt file produced by Water Q Tof. However, I don't know how > to convert those txt files to NetCDF or mzXML format which could be processed > by some software. In addition, the format of each sample is > as follows: > Each sample has 3 functions. > Function 1. Full scan data > Function > 2. Cell collision voltage data, this is developed by Waters to identify peptides. > Function 3. Lock mass data, which is used to calibrate the spectrum. > Does anybody have similar experience processing this kind of data? > > > > Many thanks. > > > > James > > > > ------------------------------ > New Yahoo! Messenger with Voice. Call regular phones from your PCand save big. > > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dankoc at gmail.com Fri Apr 7 14:04:32 2006 From: dankoc at gmail.com (Charles Danko) Date: Fri, 7 Apr 2006 14:04:32 -0400 Subject: [BiO BB] Question about obtaining gene annotation using ENSEMBL Message-ID: <8adccabf0604071104v55a56d37ie5a9eea06207fcfa@mail.gmail.com> Hi! I am trying to obtain the following information: ENSEMBL Gene ID ENSEMBL Transcript ID Transcription Start Site Translation Start Site for each transcript in the ENSEMBL database. I haven't been able to figure out how to do this using BioMart. Am I missing something? What is the easiest way to obtain this information? Thanks! Charles -------------- next part -------------- An HTML attachment was scrubbed... URL: From dmb at mrc-dunn.cam.ac.uk Thu Apr 6 18:07:07 2006 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Thu, 06 Apr 2006 23:07:07 +0100 Subject: [BiO BB] KEGG vs GO In-Reply-To: References: Message-ID: <4435910B.1080009@mrc-dunn.cam.ac.uk> Michael Ashburner (Genetics) wrote: > I think that there is some confusion in this thread. :) > 1. There is the Gene Ontology. Its terms are used (primarily) > for the annotation of gene products. Both the Ontology and the > annotations contributed by the members of the GO Consortium database > are available from the GO site. > > 2. There is the KEGG Orthology, available from the KEGG site. > This is _both_ an ontology, seen, for example, by > opening KO up to its 3rd level: http://www.genome.ad.jp/dbget-bin/get_htext?KO+-s+F+-f+F+C > _and_ annotations of classes of gene product, seen if it is opened up > to level 4: > http://www.genome.ad.jp/dbget-bin/get_htext?KO+-s+F+-f+F+D Thanks for the links, that looks useful. > It would be easy for us to make a mapping between the Gene Ontology > and KO (level 3), except that the KO includes domains outwith the GO > (e.g. 01500 Human Diseases, and its child terms). Here, "includes domains outwith the GO"? I am not sure what you mean. > In fact we will > do that and make it available as a ko2go mapping file on GO. We do not > need the "SwissProt Relational Database" to do this. Indeed, KEGG already > provide many of these mappings to the GO. Yes I see. However, when dealing with multiple classification trees or whatever, I find it very useful to start from the viewpoint of the individual gene products or genes (hence my bias towards SwissProt). In general I find it makes it easier to understand the mappings between classifications from this point of view, but of course you are right, it is not necessary. Although it would be interesting to see the underlying data (or rationale) for the mapping between GO and Kegg level 3 at the KEGG site. The ko2go file will be very interesting. > Mapping to level 4 is more problematic. The KO presents three levels: > > Ontology terms ("Levels 1-3") > e.g.: 00010 Glycolysis / Gluconeogenesis PATH:ko00010] [GO:0006096 0006094] > Families of proteins ("Level 4") > e.g. K00845 E2.7.1.2, glk; glucokinase [EC:2.7.1.2] [COG:COG0837] [GO:0004340] > Genes, whose products are members of this family > e.g. Genes HSA: 2645(GCK) > > While for those Level 4 terms that are enzymes a 'mapping' of KO to the GO > would not be hard, Do you mean between EC and the GO Molecular function branch? The above mappings at level 3 are to the Biological process branch which makes sense. > it gets more difficult further down. Consider the term: > K06051 DLL; delta > This is a child of (among others) > Notch signaling pathway [PATH:ko04330] {which would map to the GO) > and has children: > HSA: 10683(DLL3) 28514(DLL1) 54567(DLL4) > MMU: 13388(Dll1) 13389(Dll3) 54485(Dll4) > RNO: 114125(Dll3) 311332(Dll4_predicted) 84010(Dll1) > XLA: 379238(MGC52561) > DRE: 30120(dlc) 30131(dla) 30138(dld) 30141(dlb) > DME: CG3619-PA(Dmel_CG3619) > Which are clearly individual gene products. > > Thus, I conclude, that KO's: K06051 DLL; delta is a _genus_ > of gene products. This is conceptually very different from the GO, > despite what may seem to be superficial similarities. I don't understand. As you say "Notch signaling pathway" does map to go ([GO:0007219]), which has 183 assigned proteins (in my SwissProt Relational Database ;). Is this not a similar 'genus' of gene products? What do you imply by this term? SwissProt annotates some (but not all) of the genes and gene products within the K06051 'genus' with the GO:0007219 term, and in addition 103 further GO terms for those gene products (namely for Q9NYJ7, O00548, Q9NR61, Q61483, O88516, Q9JI71, O88671, P97677 and P10041). > So, contra Lucy, the difference between the GO and KO has nothing to > do with manual vs automatic annotation, or on the 'focus' of the KO, > but rather they differ in their underlying structure. But their may be a structure function relationship ;) IMHO I think integrated databases, for example the 'Bio Warehouse', http://www.biomedcentral.com/1471-2105/7/170 can provide a gold mine for investigating the relationships between different ontologies over genes and gene products, with the dual aims of consistency (error checking) and data mining. For this reason it is very interesting to compare differently derived, differently structured and differently focused ontologies at the fundamental level to look for higher level associations. However, this isn't a trivial task. A really nice software project for working with ontologies and as many different 'data models' as you can think of is here, http://www.prova.ws/ The nice thing about this project is that it makes your data and your model transparent, allowing them to be broken down or built up into other models. I think this area (data and model exchange with transparency) will become increasingly important in the field. > Michael > > > ===== > Envelope-to: ma11 at gen.cam.ac.uk > Delivery-date: Wed, 05 Apr 2006 11:14:38 +0100 > X-Cam-SpamDetails: scanned, SpamAssassin (score=0) > X-Cam-AntiVirus: No virus found > X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ > X-Original-To: bio_bulletin_board at bioinformatics.org > Delivered-To: bio_bulletin_board at bioinformatics.org > X-Cam-SpamDetails: Not scanned > X-Cam-AntiVirus: No virus found > Date: Wed, 05 Apr 2006 11:13:14 +0100 > From: Dan Bolser > User-Agent: Mozilla Thunderbird 1.0.7-1.1.fc4 (X11/20050929) > X-Accept-Language: en-us, en > MIME-Version: 1.0 > To: "The general forum at Bioinformatics.Org" > Subject: Re: [BiO BB] KEGG vs GO > Content-Transfer-Encoding: 7bit > X-BeenThere: bio_bulletin_board at bioinformatics.org > X-Mailman-Version: 2.1.5 > List-Id: "The general forum at Bioinformatics.Org" > List-Unsubscribe: , > > List-Archive: > List-Post: > List-Help: > List-Subscribe: , > > X-Keywords: > > lucifer at slimy.greenend.org.uk wrote: > >>"Samantha Fox" writes: >> >> >>>I was wondering how KEGG and GO differ from a broad perspective of >>>grouping functionally related genes. So a KEGG pathway lists all >>>genes that kind of work together, and a similar GO term would also >>>contain such > a gene list. >> >> >>IIRC, KEGG is manually created from the literature whilst GO also >>contains automatic/electronic annotation based on sequence homology. >>KEGG also focuses more on metabolic pathways, whilst GO covers a more >>comprehensive set of cellular processes and molecular functions. >> >>Hope that helps, > > > It should be possible to 'cross correlate' KEGG an GO in a number of > different ways using one of the SWISSPROT relational databases. However > you should know that generally 'ontology mapping' is an open problem :) > > Good luck! > > > >>Lucy >>-- >>Lucy McWilliam >>http://www.chiark.greenend.org.uk/~lucifer/ >>_______________________________________________ >>Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org >>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From ivenger at wisemail.weizmann.ac.il Fri Apr 7 17:51:54 2006 From: ivenger at wisemail.weizmann.ac.il (Ilya Venger) Date: Sat, 08 Apr 2006 00:51:54 +0300 Subject: [BiO BB] question on processing LC/MS data Message-ID: Hi, If you have Waters QTOF you might also have the MassLynx software. You can use the program "databridge" that comes with the Waters Masslynx software (it can be found in the "start" menu in the same tab where the MassLynx is). It is a converter between the different file formats. It will produce more than one file, the biggest one contains the relevant data. If you have any more question don't hesitate to ask. Ilya >>> janderson_net at yahoo.com 04/07/06 6:10 AM >>> Hi, I am now working on some LC/MS data (the machine is made by Waters). I have the raw data file, each sample has very large size (in the order of several G bytes). Each file has 3 functions and each function has a lot of scans with each scan corresponding to a retention time. I have 6 control samples and 6 dosed samples, the purpose is to find those proteins that are differentially expressed between the two groups (control and dose). The data is the raw txt file produced by Water Q Tof. However, I don't know how to convert those txt files to NetCDF or mzXML format which could be processed by some software. In addition, the format of each sample is as follows: Each sample has 3 functions. Function 1. Full scan data Function 2. Cell collision voltage data, this is developed by Waters to identify peptides. Function 3. Lock mass data, which is used to calibrate the spectrum. Does anybody have similar experience processing this kind of data? Many thanks. James --------------------------------- New Yahoo! Messenger with Voice. Call regular phones from your PC and save big. From janderson_net at yahoo.com Fri Apr 7 18:41:27 2006 From: janderson_net at yahoo.com (James Anderson) Date: Fri, 7 Apr 2006 15:41:27 -0700 (PDT) Subject: [BiO BB] question on processing LC/MS data In-Reply-To: Message-ID: <20060407224127.56623.qmail@web34012.mail.mud.yahoo.com> Hi, llya Thanks for your email. Unfortunately, we don't have Waters Masslynx software. I asked some people in this field, they said that Masslynx can convert those raw files (binary file) to mzXML. However, the raw data we have is not binary file, it is txt file. I don't know how to deal with this. Thanks. James Ilya Venger wrote: Hi, If you have Waters QTOF you might also have the MassLynx software. You can use the program "databridge" that comes with the Waters Masslynx software (it can be found in the "start" menu in the same tab where the MassLynx is). It is a converter between the different file formats. It will produce more than one file, the biggest one contains the relevant data. If you have any more question don't hesitate to ask. Ilya >>> janderson_net at yahoo.com 04/07/06 6:10 AM >>> Hi, I am now working on some LC/MS data (the machine is made by Waters). I have the raw data file, each sample has very large size (in the order of several G bytes). Each file has 3 functions and each function has a lot of scans with each scan corresponding to a retention time. I have 6 control samples and 6 dosed samples, the purpose is to find those proteins that are differentially expressed between the two groups (control and dose). The data is the raw txt file produced by Water Q Tof. However, I don't know how to convert those txt files to NetCDF or mzXML format which could be processed by some software. In addition, the format of each sample is as follows: Each sample has 3 functions. Function 1. Full scan data Function 2. Cell collision voltage data, this is developed by Waters to identify peptides. Function 3. Lock mass data, which is used to calibrate the spectrum. Does anybody have similar experience processing this kind of data? Many thanks. James --------------------------------- New Yahoo! Messenger with Voice. Call regular phones from your PC and save big. _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board --------------------------------- Yahoo! Messenger with Voice. Make PC-to-Phone Calls to the US (and 30+ countries) for 2?/min or less. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nuin at genedrift.org Sat Apr 8 08:11:44 2006 From: nuin at genedrift.org (Paulo Nuin) Date: Sat, 8 Apr 2006 08:11:44 -0400 Subject: [BiO BB] question on processing LC/MS data Message-ID: <20060408120906.43CB694027@primary.bioinformatics.org> Hi James I have a program that aligns GC/MS data and deals with txt files from 3 different machines (you can get it at www.genedrift.org/gasp.php). I can take a look on your data and see if I can help you, as it might similar structure. Currently my program converts Xcalibur, HP Chemstation and AMDIS txt files. Let me know if I can help Regards Paulo _____ From: bio_bulletin_board-bounces+pnuin=terra.com.br at bioinformatics.org [mailto:bio_bulletin_board-bounces+pnuin=terra.com.br at bioinformatics.org] On Behalf Of James Anderson Sent: April 7, 2006 6:41 PM To: The general forum at Bioinformatics.Org Subject: Re: [BiO BB] question on processing LC/MS data Hi, llya Thanks for your email. Unfortunately, we don't have Waters Masslynx software. I asked some people in this field, they said that Masslynx can convert those raw files (binary file) to mzXML. However, the raw data we have is not binary file, it is txt file. I don't know how to deal with this. Thanks. James Ilya Venger wrote: Hi, If you have Waters QTOF you might also have the MassLynx software. You can use the program "databridge" that comes with the Waters Masslynx software (it can be found in the "start" menu in the same tab where the MassLynx is). It is a converter between the different file formats. It will produce more than one file, the biggest one contains the relevant data. If you have any more question don't hesitate to ask. Ilya >>> janderson_net at yahoo.com 04/07/06 6:10 AM >>> Hi, I am now working on some LC/MS data (the machine is made by Waters). I have the raw data file, each sample has very large size (in the order of several G bytes). Each file has 3 functions and each function has a lot of scans with each scan corresponding to a retention time. I have 6 control samples and 6 dosed samples, the purpose is to find those proteins that are differentially expressed between the two groups (control and dose). The data is the raw txt file produced by Water Q Tof. However, I don't know how to convert those txt files to NetCDF or mzXML format which could be processed by some software. In addition, the format of each sample is as follows: Each sample has 3 functions. Function 1. Full scan data Function 2. Cell collision voltage data, this is developed by Waters to identify peptides. Function 3. Lock mass data, which is used to calibrate the spectrum. Does anybody have similar experience processing this kind of data? Many thanks. James --------------------------------- New Yahoo! Messenger with Voice. Call regular phones from your PC and save big. _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _____ Yahoo! Messenger with Voice. Make PC-to-Phone Calls to the US (and 30+ countries) for 2?/min or less. _____ E-mail classificado pelo Identificador de Spam Inteligente. Para alterar a categoria classificada, visite o Terra Mail _____ Esta mensagem foi verificada pelo E-mail Protegido Terra . Scan engine: McAfee VirusScan / Atualizado em 07/04/2006 / Vers?o: 4.4.00/4736 Proteja o seu e-mail Terra: http://mail.terra.com.br/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From MAG at Stowers-Institute.org Mon Apr 10 12:06:12 2006 From: MAG at Stowers-Institute.org (Goel, Manisha) Date: Mon, 10 Apr 2006 11:06:12 -0500 Subject: [BiO BB] Number of enzymes in each KEGG pathway Message-ID: Hi All, I am trying to do a simple analysis of a genome for which I have KEGG maps. However, I want to compare the number of proteins for each pathway in the genome of our interest and in other organisms like human, fly and worms. Is there an easy way to calculate the number of "organism specific" proteins known for each KEGG pathway ? Thanks, -Manisha -------------- next part -------------- An HTML attachment was scrubbed... URL: From bioinfosm at gmail.com Mon Apr 10 13:26:53 2006 From: bioinfosm at gmail.com (Samantha Fox) Date: Mon, 10 Apr 2006 13:26:53 -0400 Subject: [BiO BB] Number of enzymes in each KEGG pathway In-Reply-To: References: Message-ID: <726450810604101026h70db7a05j42f5ea4bdc25934@mail.gmail.com> Hey, This might be helpful : ftp://ftp.genome.jp/pub/kegg/pathways/ And then goto the specific organism you are interested in. ~S On 4/10/06, Goel, Manisha wrote: > > Hi All, > > I am trying to do a simple analysis of a genome for which I have KEGG > maps. > However, I want to compare the number of proteins for each pathway in the > genome of our interest and in other organisms like human, fly and worms. > > Is there an easy way to calculate the number of "organism specific" > proteins known for each KEGG pathway ? > > Thanks, > -Manisha > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From MAG at Stowers-Institute.org Mon Apr 10 13:45:27 2006 From: MAG at Stowers-Institute.org (Goel, Manisha) Date: Mon, 10 Apr 2006 12:45:27 -0500 Subject: [BiO BB] Number of enzymes in each KEGG pathway Message-ID: Hi Samantha, Thanks a ton for the pointer. This helps a lot.. -Manisha -----Original Message----- From: bio_bulletin_board-bounces+mag=stowers-institute.org at bioinformatics.org [mailto:bio_bulletin_board-bounces+mag=stowers-institute.org at bioinformat ics.org] On Behalf Of Samantha Fox Sent: Monday, April 10, 2006 12:27 PM To: The general forum at Bioinformatics.Org Subject: Re: [BiO BB] Number of enzymes in each KEGG pathway Hey, This might be helpful : ftp://ftp.genome.jp/pub/kegg/pathways/ And then goto the specific organism you are interested in. ~S On 4/10/06, Goel, Manisha wrote: Hi All, I am trying to do a simple analysis of a genome for which I have KEGG maps. However, I want to compare the number of proteins for each pathway in the genome of our interest and in other organisms like human, fly and worms. Is there an easy way to calculate the number of "organism specific" proteins known for each KEGG pathway ? Thanks, -Manisha _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- An HTML attachment was scrubbed... URL: From ilya.venger at weizmann.ac.il Sun Apr 9 03:16:32 2006 From: ilya.venger at weizmann.ac.il (Ilya Venger) Date: Sun, 09 Apr 2006 10:16:32 +0300 Subject: [BiO BB] question on processing LC/MS data In-Reply-To: <20060407224127.56623.qmail@web34012.mail.mud.yahoo.com> References: <20060407224127.56623.qmail@web34012.mail.mud.yahoo.com> Message-ID: <4438B4D0.7000907@weizmann.ac.il> Hi James, what software is used to acquire the data? It is possible that the same software has a plugin or an option to convert the files. Most probably the conversion will be to NetCDF. Did you try going to the sashimi project page and looking for the software there? http://sashimi.sourceforge.net/software_glossolalia.html yours, Ilya James Anderson wrote: > Hi, llya > Thanks for your email. Unfortunately, we don't have Waters Masslynx > software. I asked some people in this field, they said that Masslynx > can convert those raw files (binary file) to mzXML. However, the raw > data we have is not binary file, it is txt file. I don't know how to > deal with this. > > Thanks. > > James > > */Ilya Venger /* wrote: > > Hi, > If you have Waters QTOF you might also have the MassLynx software. You > can use the program "databridge" that comes with the Waters Masslynx > software (it can be found in the "start" menu in the same tab > where the > MassLynx is). It is a converter between the different file formats. It > will produce more than one file, the biggest one contains the relevant > data. > > If you have any more question don't hesitate to ask. > > Ilya > > >>> janderson_net at yahoo.com 04/07/06 6:10 AM >>> > > Hi, > > I am now working on some LC/MS data (the machine is made by > > Waters). I have the raw data file, each sample has very large size (in > the order > > of several G bytes). Each file has 3 functions and each function has a > lot > > of scans with each scan corresponding to a retention time. I have 6 > > control samples and 6 dosed samples, the purpose is to find those > proteins that > > are differentially expressed between the two groups (control and > dose). > The data is the raw txt file produced by Water Q Tof. However, I don't > know how > to convert those txt files to NetCDF or mzXML format which could be > processed > by some software. In addition, the format of each sample is > as follows: > Each sample has 3 functions. > Function 1. Full scan data > Function 2. Cell collision voltage data, this is developed by > Waters to > identify peptides. > Function 3. Lock mass data, which is used to calibrate the spectrum. > Does anybody have similar experience processing this kind of data? > > > > Many thanks. > > > > James > > > > --------------------------------- > New Yahoo! Messenger with Voice. Call regular phones from your PC and > save big. > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > Yahoo! Messenger with Voice. Make PC-to-Phone Calls > > to the US (and 30+ countries) for 2?/min or less. > ------------------------------------------------------------------------ > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -------------- next part -------------- An HTML attachment was scrubbed... URL: From rvm102 at york.ac.uk Mon Apr 10 13:46:09 2006 From: rvm102 at york.ac.uk (rvm102 at york.ac.uk) Date: 10 Apr 2006 18:46:09 +0100 Subject: [BiO BB] aligment of large sequences Message-ID: A really easy and powerfull tool is ACT (artemis comparison tool) available from the Sanger web site. It takes whole genome sequences, ideally from the EBI(rather then NCBI) website and graphically aligns 2 or more genomes, clearly highlighting areas of conserved synteny or deletions etc.... hope it helps :) Raju Misra (www.ecoli-york.org) From gaou at sfc.keio.ac.jp Mon Apr 10 13:52:03 2006 From: gaou at sfc.keio.ac.jp (Kazuharu Arakawa) Date: Tue, 11 Apr 2006 02:52:03 +0900 Subject: [BiO BB] Number of enzymes in each KEGG pathway In-Reply-To: References: Message-ID: <15ECD57F-FDB5-40B5-88D8-C0B6300F835A@sfc.keio.ac.jp> Hi Samantha, Also check out the KEGG API. get_enzymes_by_pathway() will fit your purpose. http://www.genome.jp/kegg/soap/doc/keggapi_manual.html#label:76 -gaou On 2006/04/11, at 4?11????2:45, Goel, Manisha wrote: > Hi Samantha, > Thanks a ton for the pointer. This helps a lot.. > -Manisha > -----Original Message----- > From: bio_bulletin_board-bounces+mag=stowers-institute.org at bioinformatics.org [mailto:bio_bulletin_board-bounces+mag=stowers-institute.org at bioinformatics.org] On Behalf Of Samantha Fox > Sent: Monday, April 10, 2006 12:27 PM > To: The general forum at Bioinformatics.Org > Subject: Re: [BiO BB] Number of enzymes in each KEGG pathway > > Hey, > This might be helpful : > ftp://ftp.genome.jp/pub/kegg/pathways/ > And then goto the specific organism you are interested in. > > ~S > > On 4/10/06, Goel, Manisha wrote: > Hi All, > > I am trying to do a simple analysis of a genome for which I have KEGG maps. > However, I want to compare the number of proteins for each pathway in the genome of our interest and in other organisms like human, fly and worms. > > Is there an easy way to calculate the number of "organism specific" proteins known for each KEGG pathway ? > > Thanks, > -Manisha > > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From lucifer at chiark.greenend.org.uk Tue Apr 11 08:34:58 2006 From: lucifer at chiark.greenend.org.uk (lucifer at chiark.greenend.org.uk) Date: Tue, 11 Apr 2006 13:34:58 +0100 Subject: [BiO BB] KEGG vs GO In-Reply-To: <20060410193738.BF5FF1C121@primary.bioinformatics.org> References: <20060410193738.BF5FF1C121@primary.bioinformatics.org> Message-ID: Michael Ashburner wrote: > So, contra Lucy, the difference between the GO and KO has nothing to > do with manual vs automatic annotation, or on the 'focus' of the KO, > but rather they differ in their underlying structure. Thanks for the clarification, Michael. I was merely offering a practical observation as to how KEGG pathways and GO processes may compare in the scope and quality of functional annotation. Samantha, if you haven't already, I recommend reading the relevant publications in the yearly database issue of Nucleic Acids Research. Obviously the most recent publications are more up-to-date, but it may be useful to read the older ones to see how both resources evolved. See http://nar.oxfordjournals.org/ Cheers, Lucy -- Lucy McWilliam http://www.chiark.greenend.org.uk/~lucifer/ From golharam at umdnj.edu Tue Apr 11 11:29:04 2006 From: golharam at umdnj.edu (Ryan Golhar) Date: Tue, 11 Apr 2006 11:29:04 -0400 Subject: [BiO BB] Theoretical Scoring Matrix Question Message-ID: <006c01c65d7c$aace1c00$e6028a0a@GOLHARMOBILE1> I've constructed a few scoring matrices for DNA sequence based on certain information. I'm now trying to determine how well they perform compared to the standard statistically based matrices, such as EDNAFULL (+5/-4) and the standard scoring matrix used by BLAST (+1/-3). My question is, what would be a valid test to compare matrices against each other? Ryan From hjm at tacgi.com Tue Apr 11 12:31:14 2006 From: hjm at tacgi.com (Harry Mangalam) Date: Tue, 11 Apr 2006 09:31:14 -0700 Subject: [BiO BB] Protein expression DB? In-Reply-To: <4438B4D0.7000907@weizmann.ac.il> References: <20060407224127.56623.qmail@web34012.mail.mud.yahoo.com> <4438B4D0.7000907@weizmann.ac.il> Message-ID: <200604110931.14559.hjm@tacgi.com> Hi All, I'm trying to create a small database for examining and correlating gene expression and protein expression for a small number of species. Gene expression data is no problem to find, but protein expression data in a manageable form is rare. I'm concentrating on coli, cerevisiae, and mammals for now. Besides the Open Proteome Database: http://apropos.icmb.utexas.edu/OPD/ GEO: http://www.ncbi.nlm.nih.gov/projects/geo/query/browse.cgi?mode=samples&filteron=8&filtervalue=3 and the Swissprot 2D gel database: http://www.expasy.org/ch2d/ NCI has some half-finished web pages that claim that data is coming, but it looks like it has been abandoned.: http://www3.cancer.gov/intra/lmp/jnw/Prot.htm are there any other obvious sources of public data available? Pointers to individual data sets would also be welcome. MS/SEQUEST summaries are especially welcome, but other text formats would also be good. Thanks in advance for your time & pointers. -- Cheers, Harry Harry J Mangalam - 949 856 2847(o) 949 285 4487(c) (email for fax) hjm at tacgi.com [plain text preferred] From basu at pharm.sunysb.edu Tue Apr 11 13:19:45 2006 From: basu at pharm.sunysb.edu (Siddhartha Basu) Date: Tue, 11 Apr 2006 13:19:45 -0400 Subject: [BiO BB] Protein expression DB? In-Reply-To: <200604110931.14559.hjm@tacgi.com> References: <20060407224127.56623.qmail@web34012.mail.mud.yahoo.com> <4438B4D0.7000907@weizmann.ac.il> <200604110931.14559.hjm@tacgi.com> Message-ID: <443BE531.7040607@pharm.sunysb.edu> Harry Mangalam wrote: > Hi All, > > I'm trying to create a small database for examining and correlating gene > expression and protein expression for a small number of species. Gene > expression data is no problem to find, but protein expression data in a > manageable form is rare. I'm concentrating on coli, cerevisiae, and mammals > for now. > > Besides the Open Proteome Database: > http://apropos.icmb.utexas.edu/OPD/ > > GEO: > http://www.ncbi.nlm.nih.gov/projects/geo/query/browse.cgi?mode=samples&filteron=8&filtervalue=3 > > and the Swissprot 2D gel database: > http://www.expasy.org/ch2d/ > > NCI has some half-finished web pages that claim that data is coming, but it > looks like it has been abandoned.: > http://www3.cancer.gov/intra/lmp/jnw/Prot.htm > > are there any other obvious sources of public data available? > > Pointers to individual data sets would also be welcome. MS/SEQUEST summaries > are especially welcome, but other text formats would also be good. > > Thanks in advance for your time & pointers. > Here is one http://www.peptideatlas.org/repository/ -sidd From marty.gollery at gmail.com Tue Apr 11 13:40:53 2006 From: marty.gollery at gmail.com (Martin Gollery) Date: Tue, 11 Apr 2006 10:40:53 -0700 Subject: [BiO BB] Theoretical Scoring Matrix Question In-Reply-To: <006c01c65d7c$aace1c00$e6028a0a@GOLHARMOBILE1> References: <006c01c65d7c$aace1c00$e6028a0a@GOLHARMOBILE1> Message-ID: Hi Ryan, Pick a number of sequence pairings, some where you know that the sequences are related and some where you know that they are not related. Your matrices should hopefully provide better discrimination than ednafull or BLAST, that is, they should provide more positive scores for the true positives and more negative scores for the known negatives. You need to do this on a large number of sequences to get a good picture- one or two is not enough. Best, Marty On 4/11/06, Ryan Golhar wrote: > > I've constructed a few scoring matrices for DNA sequence based on > certain information. I'm now trying to determine how well they perform > compared to the standard statistically based matrices, such as EDNAFULL > (+5/-4) and the standard scoring matrix used by BLAST (+1/-3). > > My question is, what would be a valid test to compare matrices against > each other? > > Ryan > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- -- Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 775-784-7042 ----------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From fazot at cs.usm.my Tue Apr 11 01:43:24 2006 From: fazot at cs.usm.my (Fazilah Othman) Date: Tue, 11 Apr 2006 13:43:24 +0800 Subject: [BiO BB] PDB format Message-ID: <200604110542.k3B5gPvE015468@cs.usm.my> Hi all, How to find the origin and 3 orthogonal vectors for coordinate system (or reference system) used in any PDB data? I have gone thru PDB format descriptions (esp. in crystallographic and coordinate transformation section), but still getting out of no where. I think the info is there, but I cannot understand or digest it correctly. I cannot find anybody familiar with PDB here in my institution. Please help. p/s:I want to try locating the same point in 2 different coordinate systems (name it csA and csB). csA is the coordinate system from the PDB file (that is what I am trying to find out) and csB is the coordinate system created by me (I have the origin and 3 orthogonal vectors). Thanks. ______________________________ -Fazot- -------------- next part -------------- An HTML attachment was scrubbed... URL: From golharam at umdnj.edu Tue Apr 11 13:50:04 2006 From: golharam at umdnj.edu (Ryan Golhar) Date: Tue, 11 Apr 2006 13:50:04 -0400 Subject: [BiO BB] Theoretical Scoring Matrix Question In-Reply-To: Message-ID: <008201c65d90$5d9f90d0$e6028a0a@GOLHARMOBILE1> Do you think a percent identity comparison be useful? In other words, how often does matrix A give a higher percent identity than matrix B? -----Original Message----- From: Martin Gollery [mailto:marty.gollery at gmail.com] Sent: Tuesday, April 11, 2006 1:41 PM To: golharam at umdnj.edu; The general forum at Bioinformatics.Org Subject: Re: [BiO BB] Theoretical Scoring Matrix Question Hi Ryan, Pick a number of sequence pairings, some where you know that the sequences are related and some where you know that they are not related. Your matrices should hopefully provide better discrimination than ednafull or BLAST, that is, they should provide more positive scores for the true positives and more negative scores for the known negatives. You need to do this on a large number of sequences to get a good picture- one or two is not enough. Best, Marty On 4/11/06, Ryan Golhar wrote: I've constructed a few scoring matrices for DNA sequence based on certain information. I'm now trying to determine how well they perform compared to the standard statistically based matrices, such as EDNAFULL (+5/-4) and the standard scoring matrix used by BLAST (+1/-3). My question is, what would be a valid test to compare matrices against each other? Ryan _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- -- Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 775-784-7042 ----------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From hjm at tacgi.com Tue Apr 11 14:26:12 2006 From: hjm at tacgi.com (Harry Mangalam) Date: Tue, 11 Apr 2006 11:26:12 -0700 Subject: [BiO BB] Protein expression DB? In-Reply-To: <443BE531.7040607@pharm.sunysb.edu> References: <20060407224127.56623.qmail@web34012.mail.mud.yahoo.com> <200604110931.14559.hjm@tacgi.com> <443BE531.7040607@pharm.sunysb.edu> Message-ID: <200604111126.12832.hjm@tacgi.com> Dang! How did I miss that??! I was all over the ISB sites... Another senior moment.. Thanks very much for the pointer - that's great!! hjm On Tuesday 11 April 2006 10:19, Siddhartha Basu wrote: > Harry Mangalam wrote: > > Hi All, > > > > I'm trying to create a small database for examining and correlating gene > > expression and protein expression for a small number of species. Gene > > expression data is no problem to find, but protein expression data in a > > manageable form is rare. I'm concentrating on coli, cerevisiae, and > > mammals for now. -- Cheers, Harry Harry J Mangalam - 949 856 2847(o) 949 285 4487(c) (email for fax) hjm at tacgi.com [plain text preferred] From MAG at Stowers-Institute.org Tue Apr 11 15:11:11 2006 From: MAG at Stowers-Institute.org (Goel, Manisha) Date: Tue, 11 Apr 2006 14:11:11 -0500 Subject: [BiO BB] Number of enzymes in each KEGG pathway Message-ID: Hi Gaou, Thanks a lot for your reply... -Manisha -----Original Message----- From: bio_bulletin_board-bounces+mag=stowers-institute.org at bioinformatics.org [mailto:bio_bulletin_board-bounces+mag=stowers-institute.org at bioinformatics.org] On Behalf Of Kazuharu Arakawa Sent: Monday, April 10, 2006 12:52 PM To: The general forum at Bioinformatics.Org Subject: Re: [BiO BB] Number of enzymes in each KEGG pathway Hi Samantha, Also check out the KEGG API. get_enzymes_by_pathway() will fit your purpose. http://www.genome.jp/kegg/soap/doc/keggapi_manual.html#label:76 -gaou On 2006/04/11, at 4?11????2:45, Goel, Manisha wrote: > Hi Samantha, > Thanks a ton for the pointer. This helps a lot.. > -Manisha > -----Original Message----- > From: > bio_bulletin_board-bounces+mag=stowers-institute.org at bioinformatics.org [mailto:bio_bulletin_board-bounces+mag=stowers-institute.org at bioinformatics.org] On Behalf Of Samantha Fox > Sent: Monday, April 10, 2006 12:27 PM > To: The general forum at Bioinformatics.Org > Subject: Re: [BiO BB] Number of enzymes in each KEGG pathway > > Hey, > This might be helpful : ftp://ftp.genome.jp/pub/kegg/pathways/ > And then goto the specific organism you are interested in. > > ?S > > On 4/10/06, Goel, Manisha wrote: Hi All, > > I am trying to do a simple analysis of a genome for which I have KEGG > maps. > However, I want to compare the number of proteins for each pathway in the genome of our interest and in other organisms like human, fly and worms. > > Is there an easy way to calculate the number of "organism specific" > proteins known for each KEGG pathway ? > > Thanks, > -Manisha > > > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From boris.steipe at utoronto.ca Tue Apr 11 17:01:28 2006 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Tue, 11 Apr 2006 17:01:28 -0400 Subject: [BiO BB] PDB format In-Reply-To: <200604110542.k3B5gPvE015468@cs.usm.my> References: <200604110542.k3B5gPvE015468@cs.usm.my> Message-ID: <5B08063D-21AC-410A-A6C0-8D1A72394559@utoronto.ca> Fazot - You have to determine the rotation matrix and translation vector that defines the relationship between your coordinate systems and then apply that to your point of interest. Hope this helps Regards, Boris On 11 Apr 2006, at 01:43, Fazilah Othman wrote: > Hi all, > > > > How to find the origin and 3 orthogonal vectors for coordinate > system (or reference system) used in any PDB data? I have gone thru > PDB format descriptions (esp. in crystallographic and coordinate > transformation section), but still getting out of no where. I think > the info is there, but I cannot understand or digest it correctly. > I cannot find anybody familiar with PDB here in my institution. > Please help. > > > > p/s:I want to try locating the same point in 2 different coordinate > systems (name it csA and csB). csA is the coordinate system from > the PDB file (that is what I am trying to find out) and csB is the > coordinate system created by me (I have the origin and 3 orthogonal > vectors). > > > > Thanks. > > ______________________________ > > -Fazot- > > > > > > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From ykalidas at gmail.com Tue Apr 11 22:01:39 2006 From: ykalidas at gmail.com (Kalidas Yeturu) Date: Wed, 12 Apr 2006 07:31:39 +0530 Subject: [BiO BB] PDB format In-Reply-To: <200604110542.k3B5gPvE015468@cs.usm.my> References: <200604110542.k3B5gPvE015468@cs.usm.my> Message-ID: <5632703b0604111901q6afcfe67o8bceff09752c4cff@mail.gmail.com> Hi Othman I have been using pdb coordinates of any atom in pdb-file as with respect to origin (0,0,0) ie., origin is not explicitly looked for in the pdb-file. Once this system is established, you can apply your own rotation/translation matrices to each coordinate. With Regards Kalidas.Y On 4/11/06, Fazilah Othman wrote: > > Hi all, > > > > How to find the* origin* and *3 orthogonal vectors* for coordinate system > (or reference system) used in any PDB data? I have gone thru PDB format > descriptions (esp. in crystallographic and coordinate transformation > section), but still getting out of no where. I think the info is there, but > I cannot understand or digest it correctly. I cannot find anybody familiar > with PDB here in my institution. Please help. > > > > p/s:I want to try locating the same point in 2 different coordinate > systems (name it csA and csB). csA is the coordinate system from the PDB > file (that is what I am trying to find out) and csB is the coordinate system > created by me (I have the origin and 3 orthogonal vectors). > > > > Thanks. > > *______________________________* > > *-Fazot-* > > > > > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > -- Kalidas Y http://ssl.serc.iisc.ernet.in/~kalidas -------------- next part -------------- An HTML attachment was scrubbed... URL: From kannaiah at bsd.uchicago.edu Thu Apr 13 14:41:22 2006 From: kannaiah at bsd.uchicago.edu (kannaiah at bsd.uchicago.edu) Date: Thu, 13 Apr 2006 13:41:22 -0500 Subject: [BiO BB] WU Blast installation Message-ID: <1144953682.443e9b5275f11@netmail.bsd.uchicago.edu> Hello, A newbie trying to learn how to work with linux systems. I Have been having trouble getting WU Blast to work. I already have Blast 2.2 working. I downloaded WUBlast 2.0. Unzipped and Untarred into a folder. I created links to the executables from a different folder. But when i try running wu_blastn from command line, it does nothing. I tried writing a wrapper script to set the ENV variables...but the ENV vars werent being set for some reason. Do you think thats the reason for it to not run? my wrapper script looks like this: ---------------------- #!/bin/bash (export BLASTDB=/biodb1/blast/ncbi/ntseq:/biodb1/blast/ncbi/pepseq;\ WUBLASTMAT=/apps/local/runtime/bin32/linux/wublast/matrix;\ WUBLASTFILTER=/apps/local/runtime/bin32/linux/wublast/filter;\ PATH=$PATH:/apps/local/runtime/bin32/linux/wublast/blastp) ------------------------------ Am i doing anything wrong or am i missing any steps? Any suggestions would be appreciated. Thanks for the help. -Kiran ------------------------------------------------- This email is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the reader of this email message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is prohibited. If you have received this email in error, please notify the sender and destroy/delete all copies of the transmittal. Thank you. ------------------------------------------------- From jeff at bioinformatics.org Thu Apr 13 14:51:47 2006 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Thu, 13 Apr 2006 14:51:47 -0400 Subject: [BiO BB] WU Blast installation In-Reply-To: <1144953682.443e9b5275f11@netmail.bsd.uchicago.edu> References: <1144953682.443e9b5275f11@netmail.bsd.uchicago.edu> Message-ID: <443E9DC3.7050207@bioinformatics.org> kannaiah at bsd.uchicago.edu wrote: > #!/bin/bash > (export BLASTDB=/biodb1/blast/ncbi/ntseq:/biodb1/blast/ncbi/pepseq;\ > WUBLASTMAT=/apps/local/runtime/bin32/linux/wublast/matrix;\ > WUBLASTFILTER=/apps/local/runtime/bin32/linux/wublast/filter;\ > PATH=$PATH:/apps/local/runtime/bin32/linux/wublast/blastp) The semicolon separates commands, so you're only exporting the first variable BLASTDB. The others won't appear in subsequent shells. Try this: #!/bin/bash export BLASTDB=/biodb1/blast/ncbi/ntseq:/biodb1/blast/ncbi/pepseq \ WUBLASTMAT=/apps/local/runtime/bin32/linux/wublast/matrix \ WUBLASTFILTER=/apps/local/runtime/bin32/linux/wublast/filter \ PATH=$PATH:/apps/local/runtime/bin32/linux/wublast/blastp Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From kannaiah at bsd.uchicago.edu Thu Apr 13 15:13:05 2006 From: kannaiah at bsd.uchicago.edu (kannaiah at bsd.uchicago.edu) Date: Thu, 13 Apr 2006 14:13:05 -0500 Subject: [BiO BB] WU Blast installation In-Reply-To: <443E9DC3.7050207@bioinformatics.org> References: <1144953682.443e9b5275f11@netmail.bsd.uchicago.edu> <443E9DC3.7050207@bioinformatics.org> Message-ID: <1144955585.443ea2c131c21@netmail.bsd.uchicago.edu> Hi Jeff, I tried what you suggested. But didnt work. I also tried with export in front of every variable, that didnt work either:( -Kiran Quoting "J.W. Bizzaro" : > kannaiah at bsd.uchicago.edu wrote: > > #!/bin/bash > > (export BLASTDB=/biodb1/blast/ncbi/ntseq:/biodb1/blast/ncbi/pepseq;\ > > WUBLASTMAT=/apps/local/runtime/bin32/linux/wublast/matrix;\ > > WUBLASTFILTER=/apps/local/runtime/bin32/linux/wublast/filter;\ > > PATH=$PATH:/apps/local/runtime/bin32/linux/wublast/blastp) > > The semicolon separates commands, so you're only exporting the first variable > > BLASTDB. The others won't appear in subsequent shells. Try this: > > #!/bin/bash > export BLASTDB=/biodb1/blast/ncbi/ntseq:/biodb1/blast/ncbi/pepseq \ > WUBLASTMAT=/apps/local/runtime/bin32/linux/wublast/matrix \ > WUBLASTFILTER=/apps/local/runtime/bin32/linux/wublast/filter \ > PATH=$PATH:/apps/local/runtime/bin32/linux/wublast/blastp > > Jeff > -- > J.W. Bizzaro > Bioinformatics Organization, Inc. (Bioinformatics.Org) > E-mail: jeff at bioinformatics.org > Phone: +1 508 890 8600 > -- > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > ------------------------------------------------- This email is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the reader of this email message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is prohibited. If you have received this email in error, please notify the sender and destroy/delete all copies of the transmittal. Thank you. ------------------------------------------------- From jeff at bioinformatics.org Thu Apr 13 15:23:52 2006 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Thu, 13 Apr 2006 15:23:52 -0400 Subject: [BiO BB] WU Blast installation In-Reply-To: <1144955585.443ea2c131c21@netmail.bsd.uchicago.edu> References: <1144953682.443e9b5275f11@netmail.bsd.uchicago.edu> <443E9DC3.7050207@bioinformatics.org> <1144955585.443ea2c131c21@netmail.bsd.uchicago.edu> Message-ID: <443EA548.8060707@bioinformatics.org> I guess that's not the problem, then :-) But what do you mean "it does nothing"? Does the shell command prompt re-appear after typing the command or not? Are there any error messages? Have you read the manual on how to run it? Also, have you tried asking for help on the WU Blast mailing list (if there is one)? Jeff kannaiah at bsd.uchicago.edu wrote: > Hi Jeff, > > I tried what you suggested. But didnt work. I also tried with export in front of > every variable, that didnt work either:( > > -Kiran -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From kannaiah at bsd.uchicago.edu Thu Apr 13 16:10:44 2006 From: kannaiah at bsd.uchicago.edu (kannaiah at bsd.uchicago.edu) Date: Thu, 13 Apr 2006 15:10:44 -0500 Subject: [BiO BB] WU Blast installation In-Reply-To: <443EA548.8060707@bioinformatics.org> References: <1144953682.443e9b5275f11@netmail.bsd.uchicago.edu> <443E9DC3.7050207@bioinformatics.org> <1144955585.443ea2c131c21@netmail.bsd.uchicago.edu> <443EA548.8060707@bioinformatics.org> Message-ID: <1144959044.443eb044201c5@netmail.bsd.uchicago.edu> Well, i got the program to run. But the ENV variables arent being setup. It is just ignoring the "export" command. Anyway, i will try writing to the WUBlast guys, and see what they have to say. thank you for the help. -Kiran Quoting "J.W. Bizzaro" : > I guess that's not the problem, then :-) But what do you mean "it does > nothing"? Does the shell command prompt re-appear after typing the command > or > not? Are there any error messages? Have you read the manual on how to run > it? > Also, have you tried asking for help on the WU Blast mailing list (if there > > is one)? > > Jeff > > kannaiah at bsd.uchicago.edu wrote: > > Hi Jeff, > > > > I tried what you suggested. But didnt work. I also tried with export in > front of > > every variable, that didnt work either:( > > > > -Kiran > > -- > J.W. Bizzaro > Bioinformatics Organization, Inc. (Bioinformatics.Org) > E-mail: jeff at bioinformatics.org > Phone: +1 508 890 8600 > -- > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > ------------------------------------------------- This email is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the reader of this email message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is prohibited. If you have received this email in error, please notify the sender and destroy/delete all copies of the transmittal. Thank you. ------------------------------------------------- From christoph.gille at charite.de Tue Apr 18 13:52:59 2006 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Tue, 18 Apr 2006 19:52:59 +0200 (CEST) Subject: [BiO BB] blast against Mutation database Message-ID: <61483.84.190.55.52.1145382779.squirrel@webmail.charite.de> I have a bunch of AA sequences and want to identify all reported point mutations (single AA substitutions) in men or other organisms in all proteins related to these sequences. Is there a service for a batch blast against mutation databases ? Or can one download the sequences of mutation databases to perform the BLAST locally? Many thanks for your help From lichunjiang at sibs.ac.cn Wed Apr 19 21:24:49 2006 From: lichunjiang at sibs.ac.cn (lichunjiang) Date: Thu, 20 Apr 2006 09:24:49 +0800 (CST) Subject: [BiO BB] blast against Mutation database In-Reply-To: <61483.84.190.55.52.1145382779.squirrel@webmail.charite.de> References: <61483.84.190.55.52.1145382779.squirrel@webmail.charite.de> Message-ID: <2751.10.10.224.88.1145496289.squirrel@webmail.sibs.ac.cn> Dear Christoph Gille, I know the following website include a PMD(protein mutation database) and can be searched with multiple query FASTA sequences. While I haven't try it myself. http://www.genome.jp/dbget/dbget_url.html http://www.genome.ad.jp/dbget/ Best wishes, Lichun Jiang Dr. Christoph Gille wrote: > I have a bunch of AA sequences and want to identify all reported > point mutations (single AA substitutions) > in men or other organisms in all proteins related to these sequences. > Is there a service for a batch blast against mutation databases ? > Or can one download the sequences of mutation databases to perform the > BLAST > locally? > Many thanks for your help > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -- lichunjiang at sibs.ac.cn Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences -------------- next part -------------- An HTML attachment was scrubbed... URL: From areed at imdc.org Tue Apr 25 13:09:27 2006 From: areed at imdc.org (Ann Reed) Date: Tue, 25 Apr 2006 12:09:27 -0500 Subject: [BiO BB] Education: Tuition-free online bioinformatics training seeking students Message-ID: <7BDF6464945AB045B845C2AB588B9B401B88E5@tachyon.imdc.org> BiTmaP: Bioinformatics Training Program is seeking students for the Fall 2006 semester. The application deadline is June 9, 2006. All tuition and course materials are paid for by a generous grant from the U.S. Dept. of Labor. BiTmaP courses are accredited and provided by the University of Illinois at Chicago (UIC). Our program consists of on-line lectures, industry seminars and work-site and internship experiences that focus on standard bioinformatics principles and protocols used widely throughout industry and academia. Students complete 3 of the following 4 courses and earn 12-graduate level credits and a certificate in bioinformatics from UIC. BiTmaP courses are: Introduction to Bioinformatics, Biostatistics, Functional Computational Genomics and Microarray, Molecular Modeling in Bioinformatics. Minimum qualifications for applicants: 1. U.S. Citizenship or Permanent Residency 2. Minimum B.S. degree, preferably in C.S. 3. Minimum 3.0 or B average GPA 4. Aptitude, enthusiasm or interest in moving to a career in the life sciences. To pre-qualify for tuition sponsorship, send a resume or CV to apply at bitmapchicago.com. For more information, please visit http://www.bitmapchicago.com/ or email areed at bitmapchicago.com. This program is intended to help re-train American workers, so U.S. citizenship or permanent residency is required. Ann Reed Director, BiTmaP: Bioinformatics Training Program Chicago Technology Park 312.243.1289 www.BiTmaPchicago.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From aalibes at cnio.es Wed Apr 26 06:28:38 2006 From: aalibes at cnio.es (=?ISO-8859-1?Q?Andreu_Alib=E9s?=) Date: Wed, 26 Apr 2006 12:28:38 +0200 Subject: [BiO BB] 2006 Summer School: Biophysics of Biological Circuits, Madrid Message-ID: <444F4B56.4030005@cnio.es> -------- Original Message -------- Subject: 2006 Summer School: Biophysics of Biological Circuits, Madrid Date: Wed, 26 Apr 2006 12:25:53 +0200 From: Poyatos.Juan_Fernando Dear all, we are organising a summer school focused on the new recently developed quantitative/biophysical approaches to understand the organization and function of biological networks (see below for a more detail information). I thought that some people here could be interested. cheers, - juan Ps, please feel free to distribute this information to those you might consider to be interested, ----------------------------------------------------------------------------------------------------------------- From: Juan F. Poyatos Subject: 2006 Summer School: Biophysics of Biological Circuits, Madrid 2006 summer school "BIOPHYSICS OF BIOLOGICAL CIRCUITS: FROM MOLECULES TO NETWORKS" 19-22 September 2006, Residencia La Cristalera, Miraflores de la Sierra (Madrid, Spain) Registration dead-line: June 30th Further information: Instituto de Ciencia de Materiales "Nicolas Cabrera" http://www.uam.es/otroscentros/inc/summerschools/summerschool2006/index.html GOALS The school is planed for participants coming from different disciplines but with strong interest in Biophysics. Our goal is to introduce them to some relevant biological problems for which a physical approach, conceptual as well as experimental, has firmly contributed to their understanding. To this end, we have divided the School in three sections sharing a common framework: the view of biological networks as modular assemblies where the properties of individual elements as well as the behavior of the modules can be studied with present day experimental techniques. The topics included in this course are divided according to the following categories: Biophysics of genetic networks: Design principles of genetic circuits, noise in gene expression, regulation and control of genetic networks. Biophysics of neuronal circuits: Dynamics of neural networks, olfactory processing, problems in visual attention. Biophysics of individual molecules: Biophysics of molecular motors, biomechanics, behavior of single molecules in living cells. -- Juan F. Poyatos Structural and Computational Biology Programme Spanish National Cancer Centre (CNIO) Melchor Fernandez Almagro, 3/E-28029 Madrid SPAIN Phone:+34 917 328 009/Fax: +34 912 246 976 http://bioinfo.cnio.es/~jpoyatos **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From afsanehmotamed at yahoo.com Tue Apr 25 13:53:03 2006 From: afsanehmotamed at yahoo.com (Afsaneh Motamed-Khorasani) Date: Tue, 25 Apr 2006 13:53:03 -0400 (EDT) Subject: [BiO BB] Education: Tuition-free online bioinformatics training seeking students In-Reply-To: <7BDF6464945AB045B845C2AB588B9B401B88E5@tachyon.imdc.org> Message-ID: <20060425175303.7971.qmail@web88106.mail.re2.yahoo.com> Hi, I have all other requirements you asked for this grant except for being a US citizen. I am a Canadaian citizen and I am planning to come over to US and reside there for my job. Can I use any exemption in my case. I already have a PhD from life sciences and I worked closely with microarray, affymetrix, real-time PCR, Tissue microaaray and lots of high troughput methods of protein screening. This course will be extremely useful for me and I would be really appreciative if I can use it toward my goal to become an expert scientist in bioinformatics. Please notify me if I am eligible so that I can send you my CV. I just got the approval for my paper to be published in Oncogene reagrding all these bioinformatics I did for my PhD. Thanks, Afsaneh Ann Reed wrote: BiTmaP: Bioinformatics Training Program is seeking students for the Fall 2006 semester. The application deadline is June 9, 2006. All tuition and course materials are paid for by a generous grant from the U.S. Dept. of Labor. BiTmaP courses are accredited and provided by the University of Illinois at Chicago (UIC). Our program consists of on-line lectures, industry seminars and work-site and internship experiences that focus on standard bioinformatics principles and protocols used widely throughout industry and academia. Students complete 3 of the following 4 courses and earn 12-graduate level credits and a certificate in bioinformatics from UIC. BiTmaP courses are: Introduction to Bioinformatics, Biostatistics, Functional Computational Genomics and Microarray, Molecular Modeling in Bioinformatics. Minimum qualifications for applicants: 1. U.S. Citizenship or Permanent Residency 2. Minimum B.S. degree, preferably in C.S. 3. Minimum 3.0 or B average GPA 4. Aptitude, enthusiasm or interest in moving to a career in the life sciences. To pre-qualify for tuition sponsorship, send a resume or CV to apply at bitmapchicago.com. For more information, please visit http://www.bitmapchicago.com/ or email areed at bitmapchicago.com. This program is intended to help re-train American workers, so U.S. citizenship or permanent residency is required. Ann Reed Director, BiTmaP: Bioinformatics Training Program Chicago Technology Park 312.243.1289 www.BiTmaPchicago.com _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board --------------------------------- Enrich your life at Yahoo! Canada Finance -------------- next part -------------- An HTML attachment was scrubbed... URL: From Reactome-Knowledgebase at reactome.org Mon Apr 24 11:42:25 2006 From: Reactome-Knowledgebase at reactome.org (Reactome-Knowledgebase at reactome.org) Date: Mon, 24 Apr 2006 11:42:25 -0400 Subject: [BiO BB] Reactome version 17 released! Message-ID: The Reactome Knowledgebase group (Cold Spring Harbor Lab and the European Bioinformatics Institute) is proud to announce the release of Reactome Version 17 today, accessible at http://www.reactome.org! Reactome is a curated knowledgebase of biological processes in humans. It covers processes ranging from basic pathways of metabolism to complex events such as hormonal signaling and apoptosis. The information in Reactome is provided by expert bench biologists, and edited and managed as a relational database by the Reactome staff. New material is peer-reviewed and revised as necessary before publication to the web. Reactome entries are linked to corresponding ones in NCBI EntrezGene, RefSeq, OMIM, Ensembl genome annotations, UCSC Genome Browser, KEGG, ChEBI and Gene Ontology (GO). New modules include signaling cascades mediated by TGF-beta, RIG-I, and Toll-like receptors 3 and 4, the conjugation phase of xenobiotic metabolism, aspects of the metabolism of lipoproteins, cell cycle regulation by the anaphase-promoting complex (APC), and ATR activation in response to replication stress. The total number of curated human reactions in the knowledgebase is now 1828 and the total number of annotated human proteins is 1369. New software features in version 17 include an upgraded SkyPainter tool, which now shows all reactions involving proteins in a user- specified list highlighted on the Reactome reaction map, lists these reactions in downloadable tabular form, and identifies pathways that are statistically over-represented for a list of specified proteins. As before, Reactome data can be exported in SMBL, Prot?g?, and BioPAX level 2 formats. Like everything in Reactome, these downloaded and exported materials can be reused and redistributed freely. For questions and comments, please reply to this message or write to help at reactome.org -Reactome teams at CSHL and EBI -------------- next part -------------- An HTML attachment was scrubbed... URL: From phoebe at deakin.edu.au Wed Apr 26 09:40:37 2006 From: phoebe at deakin.edu.au (Phoebe Chen) Date: Wed, 26 Apr 2006 23:40:37 +1000 Subject: [BiO BB] First Call for Papers - APBC 2007 in Hong Kong Message-ID: <1146058837.444f7855a9ad3@mail.deakin.edu.au> ============================================ FIRST CALL FOR PAPERS - APBC 2007 The Fifth Asia-Pacific Bioinformatics Conference, APBC2007, will be held in Hong Kong during 15 - 17 January 2007. See http://www.cs.hku.hk/apbc2007. =========================================== The Asia-Pacific Bioinformatics Conference series is an annual forum for exploring research, development, and novel applications bioinformatics. The aim of this conference is to bring together researchers, professionals, and industrial practitioners for interaction and exchange of knowledge and ideas. We invite submissions that address conceptual and practical issues of bioinformatics. TOPICS OF INTEREST Typical, but not exclusive, topics of interest include: Sequence analysis Motif Finding Recognition of Genes RNA Analysis Population genetics/SNP/Haplotyping Physical and Genetic Mapping Comparative Genomics, Genome rearrangements Evolution and Phylogeny Protein structure analysis Microarray design Proteomics Transcriptome, Gene Expression Pathways, Networks and Systems Databases and Data Integration Ontologies Text Mining Applications IMPORTANT DATES Submission of papers: Jul 15, 2006 Notification of paper acceptance: Sep 15, 2006 Submission of posters: Sep 30, 2006 Camera-ready copy & Author registration: Oct 10, 2006 Notification of poster acceptance: Oct 20, 2006 Conference: Jan 15 - 17, 2007 CONFERENCE CHAIR Francis YL Chin, The University of Hong Kong, Hong Kong PROGRAM CHAIRS David Sankoff, The University of Ottawa Lusheng Wang, The City University of Hong Kong PROGRAM COMMITTEE Tatsuya Akutsu, Miguel Andrade,Stephane Aris-Brosou, Joel Bader, Serafim Batzoglou, David Bryan,Jeremy Buhler, Peter Donnelly, Dannie Durand, Nadia El-Mabrouk, Robert Giegerich, Carole Goble, Concettina Guerra, Dan Gusfield, Michael Hallett, Sridhar Hannenhalli, Daniel Huson, Gavin Huttley, Jenn-Kang Hwang, Tao Jiang, Uri Keich, Anand Kumar, Tak Wah Lam, Doheon Lee, Jinyan Li, Wentian Li, Guohui Lin, Michal Linial, Zhejie Liu, Bin Ma, Satoru Miyano, Laxmi Parida, Mark Ragan, Marie-France Sagot, Akinori Sarai, Vincent Schachter, Steven Skiena, Yun Song, Robert Stevens, Alfonso Valencia, Michael Waterman, Ken Wolfe, Stacia Wyman, Hong Yan, Qiang Yang, Kaizhong Zhang, Liqing Zhang, Louxin Zhang STEERING COMMITTEE Phoebe Chen (Chair), Deakin University, Australia Sang Yup Lee, KAIST, Korea Satoru Miyano, University of Tokyo, Japan Mark Ragan, University of Queensland, Australia Limsoon Wong, National University of Singapore SUBMISSION GUIDELINES APBC2007 invites high-quality original papers on any topic related to Bioinformatics. Papers should be no more than 10 pages in length conforming to the formatting instructions for the series Advances in Bioinformatics & Computational Biology (instructions available at the APBC2007 website). Papers will be judged on originality, significance, correctness, and clarity. Authors should submit a PDF file according to the instructions on the APBC2007 Paper Submission Website. The full paper must be submitted by 15 July 2006. The proceedings will be published as a volume in the series Advances in Bioinformatics & Computational Biology by Imperial College Press. Expanded version of the best papers will be invited for publication in the Journal of Bioinformatics and Computational Biology. Inclusion of a paper in the proceedings is contingent on one of the authors registering and presenting at the conference. From 3Dsig06 at weizmann.ac.il Thu Apr 27 14:16:49 2006 From: 3Dsig06 at weizmann.ac.il (3Dsig06) Date: Thu, 27 Apr 2006 21:16:49 +0300 (IDT) Subject: [BiO BB] Approaching deadlines - 3Dsig: Structural Bioinformatics & Computational Biophysics Message-ID: <1437.130.91.65.163.1146161809.squirrel@130.91.65.163> 3Dsig: A Structural Bioinformatics and Computational Biophysics satellite meeting of the ISMB conference will take place on August 4-5, at Fortaleza, BRAZIL. http://3dsig.weizmann.ac.il/ Active participants in 3Dsig's program and/or scientific committee include: Phil Bourne, Steven Brenner, Wah Chiu, John Moult, Jeff Saven, Joel Sussman and Janet Thornton. Our May 1st DEADLINE IS APPROACHING including: 1. Call for abstracts: Most 3Dsig oral presentations will be selected from submitted abstracts. Unique features of 3Dsig's abstracts include: (a) All accepted abstract will be presented via the medium of laptop in our well-organized and successful LAPTOP SESSION (replacing the traditional poster session). (b) Abstract submission includes a 'representative figure' serving as an icon to the abstract. In addition to the name tag, each abstract submitter will receive a badge with the representative figure thus facilitating informal scientific mingling. (c) Abstracts will be posted on the new 3Dsig discussion forum allowing participants to engage in lively scientific discussions prior to the meeting. 2. Travel fellowship ? We encourage students and postDocs to enjoy the significant number of travel fellowships available by our parent ISMB conference. Note, travel fellowships are meant for the ISMB parent conference. 3. ISMB PLoS-track oral presentation and poster abstracts. This track allows one to submit an abstract that may be selected for oral presentation at ISMB while reserving first publication for another forum. * Note, you may choose, to register to 3Dsig and NOT to ISMB. If you choose to attend both meetings, you should submit the abstract to ISMB and 3Dsig separately. Links to these approaching deadlines as well as exciting sponsorship opportunities and information on 3Dsig's topics and format are available at: http://3dsig.weizmann.ac.il/ Looking forward to meeting you at 3Dsig, 3Dsig committees ________________________________ 3Dsig: Structural Bioinformatics & Computational Biophysics Meeting 4-5 Aug. 2006, Fortaleza, Brazil Between the ISMB and SwissProt20 Conferences http://3dsig.weizmann.ac.il 3dsig06 [at] weizmann.ac.il From drlivesay at csupomona.edu Thu Apr 27 15:20:13 2006 From: drlivesay at csupomona.edu (Dr. Dennis R. Livesay) Date: Thu, 27 Apr 2006 12:20:13 -0700 Subject: [BiO BB] Postdoctoral Research Associate Positions in Bioinformatics Message-ID: <0884387A56F94E469988DFD7D01097BF8AC187@EXCH01.win.csupomona.edu> Applications are invited for a postdoctoral Research Associate positions in the lab of Prof. Dennis R. Livesay starting approximately August 2006. A current challenge of bioinformatics is to be able to predict protein functional sites from sequence and structure. This project builds upon prior success of phylogenetic motifs (PMs) to identify functional regions from sequence. PMs are alignment fragments that mirror the overall familial phylogeny (see La et al., Proteins, 2005 and La & Livesay, BMC Bioinformatics, 2005). One of the primary goals of this project is to extend the PM approach to identify specific catalytic sites (versus functional site regions) using a neural network and/or machine learning approach. Also, the successful candidate will be expected to learn and apply a wide variety of other state-of-the-art functional site prediction techniques, including: evolutionary trace, ConSurf, topology-based approaches, strain energy-based approaches, etc. Candidates should be highly motivated with a Ph.D. in Bioinformatics, Biology, Computer Science or related discipline. Candidates should have prior experience in the area of Bioinformatics and/or Computational Biophysics with a demonstrated ability to conduct research independently. Demonstrated knowledge of basic sequence and structure analysis techniques is required. Candidates are also expected to have strong programming skills. Knowledge of UNIX/LINUX operating systems is essential; prior experience with grid/cluster computing is considered a bonus, but not absolutely required. Prior experience with database design, MySQL and CGI programming is also desired. More information can be obtained at http://www.csupomona.edu/~drlivesay. Note that starting in August, Prof. Livesay will be moving his lab to the Bioinformatics Research Center at the University of North Carolina at Charlotte, which is where the successful candidate will be employed. Applicants interested in applying should send curriculum vitae and graduate transcripts (a copy is okay) to Prof. Dennis R. Livesay, Dept. of Chemistry, Cal Poly Pomona, 3801 W. Temple Ave, Pomona, CA 91768 or electronically to drlivesay at csupomona.edu. Applicants should also arrange for three letters of reference to be sent to the same address; applicants should not send reference letters themselves. Full consideration will be to applications received before June 1, 2006. UNC-Charlotte is an EOE/AA employer. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Dennis R. Livesay Associate Professor & Graduate Coordinator Department of Chemistry, Cal Poly Pomona 909.869.4409 (office), 909.869.4344 (fax) http://www.csupomona.edu/~drlivesay From dankoc at gmail.com Thu Apr 27 15:11:51 2006 From: dankoc at gmail.com (Charles Danko) Date: Thu, 27 Apr 2006 15:11:51 -0400 Subject: [BiO BB] Quick question on choosing clusters ... Message-ID: <8adccabf0604271211y71be766ava94cf772b4204ee3@mail.gmail.com> Hi, I am using hierarchical agglomerative clustering, but need to split clusters once they are identified. Is there some way that I can determine the optimal number of clusters to use for my data set? Is there a function in R that I can use for this purpose? Thanks! -------------- next part -------------- An HTML attachment was scrubbed... URL: From mahef111 at link.net Wed Apr 26 09:40:01 2006 From: mahef111 at link.net (Mhmoud Elhefnawi) Date: Wed, 26 Apr 2006 15:40:01 +0200 Subject: [BiO BB] software for sequence mutational analysis Message-ID: <000001c66acf$29cec8b0$6298c952@pc> Dear colleagues, I have some sequences closely related that I want to perform mutationl analysis in an efficient way, locating mutations locations, frequency of mutations, ...etc.. Is there some package that can help me with that? Thanks in advance for helping, Mahmoud -------------- next part -------------- An HTML attachment was scrubbed... URL: From rakeshmotani at rediffmail.com Fri Apr 28 00:05:53 2006 From: rakeshmotani at rediffmail.com (Rakesh Motani) Date: Thu, 27 Apr 2006 23:05:53 -0500 Subject: [BiO BB] superimposition trouble Message-ID: <445194A1.3090707@rediffmail.com> Hi, I am a new user for SwissPDB viewer. I am trying to superimpose 2 structures. They have almost same sequence just 1amino acid difference. Before superimposing (ie using fit--> itterative magic fit command) I can see that both are same. After using the fit command I mentioned part of the second sequence in superimpostion disappears and they don't fit well. I would be great if Ican get some suggestions on this. I thinks it's a software issue. John From pjain at xldb.di.fc.ul.pt Fri Apr 28 05:09:35 2006 From: pjain at xldb.di.fc.ul.pt (Pooja Jain) Date: Fri, 28 Apr 2006 10:09:35 +0100 Subject: [BiO BB] Domain Prediction Message-ID: <1146215375.4451dbcf36680@webservices.di.fc.ul.pt> Hello everybody, I have sequenced a protein for which no structural signature can be found in PDB. I plan to identify domains in it. For this shall I BLAST it against Pfam or some other database ? Ulternatively, can anyone suggest the most accurate de novo or sequence similarity based domain prediction tool ? Thank you in advance. -Pooja From boris.steipe at utoronto.ca Fri Apr 28 11:04:47 2006 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Fri, 28 Apr 2006 11:04:47 -0400 Subject: [BiO BB] Domain Prediction In-Reply-To: <1146215375.4451dbcf36680@webservices.di.fc.ul.pt> References: <1146215375.4451dbcf36680@webservices.di.fc.ul.pt> Message-ID: <877636A8-2C6C-481D-8734-69C1440C7812@utoronto.ca> If you want to compare your sequence against known domains, you can use RPS-Blast http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi or try a HMMER search against the SMART database http://smart.embl-heidelberg.de/smart/set_mode.cgi?NORMAL=1 HTH, Boris On 28 Apr 2006, at 05:09, Pooja Jain wrote: > Hello everybody, > > I have sequenced a protein for which no structural signature can be > found in > PDB. I plan to identify domains in it. For this shall I BLAST it > against Pfam > or some other database ? Ulternatively, can anyone suggest the most > accurate de > novo or sequence similarity based domain prediction tool ? > > Thank you in advance. > > -Pooja > > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From natarajanganesan at gmail.com Fri Apr 28 14:52:36 2006 From: natarajanganesan at gmail.com (Natarajan Ganesan) Date: Fri, 28 Apr 2006 14:52:36 -0400 Subject: [BiO BB] Re: Latest Internet explorer 7.0 doesnt support "LINK"out tool in NCBI's 'nucleotide' and 'protein' bank Message-ID: <001201c66af4$ead37950$bff0a18d@georgetown.mei.georgetown.edu> This message is for those who are familiar with using the 'Links' facility when searching for 'nucleotide' OR 'protein' sequences. Normally one sees a popup that links the particular result across a panel of NCBI services. This worked well in IE6.0. However the latest IE7.0 beta seems to have an error that prevents this popup. I believe this will be soon rectified by the NCBI, but till then sticking with IE6.0 is good. Natarajan Ganesan Email: ng6 at georgetown.edu Homepage: http://www.georgetown.edu/faculty/ng6/ -----Original Message----- From: J.W. Bizzaro [mailto:jeff at bioinformatics.org] Sent: Friday, April 28, 2006 12:39 PM To: ng6 at georgetown.edu Subject: Re: Latest Internet explorer 7.0 doesnt support "LINK"out tool in 'nucleotide' and 'protein' bank Hi Natarajan, You might want to post this to the BiO Bulletin Board instead: bbb at bioinformatics.org Thanks, Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From ivenger at wisemail.weizmann.ac.il Fri Apr 28 14:56:14 2006 From: ivenger at wisemail.weizmann.ac.il (Ilya Venger) Date: Fri, 28 Apr 2006 21:56:14 +0300 Subject: [BiO BB] Quick question on choosing clusters ... Message-ID: Hi, There is no really good way for choosing an optimal number of clusters. It very much depends on the nature of the data itself. Some algorithms exist such that involve computing mean split silhouette and computing the within and across cluster variability, but none will give you a really definite answer, they can only point to local minima that you are better off with. For example, you might see that 4 clusters are better than 3 or 5, but also that 12 is better than 13 and 11, but you wouldn't realy know, which is beter, 4 or 12. As I said you need to know your data well and know how many clusters in general you expect. You might also want to employ some sorting algorithms (such as Eytan Domani's SPIN) first, in order to visualize and observe the structure of your data. I think that MSS was implemented some time in R, but you will need to check it. Hope this helps, Ilya >>> dankoc at gmail.com 04/27/06 10:11 PM >>> Hi, I am using hierarchical agglomerative clustering, but need to split clusters once they are identified. Is there some way that I can determine the optimal number of clusters to use for my data set? Is there a function in R that I can use for this purpose? Thanks! From golharam at umdnj.edu Fri Apr 28 15:06:50 2006 From: golharam at umdnj.edu (Ryan Golhar) Date: Fri, 28 Apr 2006 15:06:50 -0400 Subject: [BiO BB] Re: Latest Internet explorer 7.0 doesnt support "LINK"outtool in NCBI's 'nucleotide' and 'protein' bank In-Reply-To: <001201c66af4$ead37950$bff0a18d@georgetown.mei.georgetown.edu> Message-ID: <031001c66af6$e84ff0d0$2f01a8c0@GOLHARMOBILE1> Does it work with Firefox/Mozilla? -----Original Message----- From: bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org [mailto:bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org ] On Behalf Of Natarajan Ganesan Sent: Friday, April 28, 2006 2:53 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Re: Latest Internet explorer 7.0 doesnt support "LINK"outtool in NCBI's 'nucleotide' and 'protein' bank Importance: High This message is for those who are familiar with using the 'Links' facility when searching for 'nucleotide' OR 'protein' sequences. Normally one sees a popup that links the particular result across a panel of NCBI services. This worked well in IE6.0. However the latest IE7.0 beta seems to have an error that prevents this popup. I believe this will be soon rectified by the NCBI, but till then sticking with IE6.0 is good. Natarajan Ganesan Email: ng6 at georgetown.edu Homepage: http://www.georgetown.edu/faculty/ng6/ -----Original Message----- From: J.W. Bizzaro [mailto:jeff at bioinformatics.org] Sent: Friday, April 28, 2006 12:39 PM To: ng6 at georgetown.edu Subject: Re: Latest Internet explorer 7.0 doesnt support "LINK"out tool in 'nucleotide' and 'protein' bank Hi Natarajan, You might want to post this to the BiO Bulletin Board instead: bbb at bioinformatics.org Thanks, Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From natarajanganesan at gmail.com Fri Apr 28 16:15:24 2006 From: natarajanganesan at gmail.com (Natarajan Ganesan) Date: Fri, 28 Apr 2006 16:15:24 -0400 Subject: [BiO BB] Re: Latest Internet explorer 7.0 doesnt support"LINK"outtool in NCBI's 'nucleotide' and 'protein' bank In-Reply-To: <031001c66af6$e84ff0d0$2f01a8c0@GOLHARMOBILE1> Message-ID: <001901c66b00$7bf9d360$bff0a18d@georgetown.mei.georgetown.edu> Yes, it does. I checked it. Natarajan -----Original Message----- From: bio_bulletin_board-bounces+natarajanganesan=gmail.com at bioinformatics.org [mailto:bio_bulletin_board-bounces+natarajanganesan=gmail.com at bioinformatics .org] On Behalf Of Ryan Golhar Sent: Friday, April 28, 2006 3:07 PM To: 'The general forum at Bioinformatics.Org' Subject: RE: [BiO BB] Re: Latest Internet explorer 7.0 doesnt support"LINK"outtool in NCBI's 'nucleotide' and 'protein' bank Does it work with Firefox/Mozilla? -----Original Message----- From: bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org [mailto:bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org ] On Behalf Of Natarajan Ganesan Sent: Friday, April 28, 2006 2:53 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Re: Latest Internet explorer 7.0 doesnt support "LINK"outtool in NCBI's 'nucleotide' and 'protein' bank Importance: High This message is for those who are familiar with using the 'Links' facility when searching for 'nucleotide' OR 'protein' sequences. Normally one sees a popup that links the particular result across a panel of NCBI services. This worked well in IE6.0. However the latest IE7.0 beta seems to have an error that prevents this popup. I believe this will be soon rectified by the NCBI, but till then sticking with IE6.0 is good. Natarajan Ganesan Email: ng6 at georgetown.edu Homepage: http://www.georgetown.edu/faculty/ng6/ -----Original Message----- From: J.W. Bizzaro [mailto:jeff at bioinformatics.org] Sent: Friday, April 28, 2006 12:39 PM To: ng6 at georgetown.edu Subject: Re: Latest Internet explorer 7.0 doesnt support "LINK"out tool in 'nucleotide' and 'protein' bank Hi Natarajan, You might want to post this to the BiO Bulletin Board instead: bbb at bioinformatics.org Thanks, Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From golharam at umdnj.edu Fri Apr 28 19:17:16 2006 From: golharam at umdnj.edu (Ryan Golhar) Date: Fri, 28 Apr 2006 19:17:16 -0400 Subject: [BiO BB] Re: Latest Internet explorer 7.0 doesnt support"LINK"outtool in NCBI's 'nucleotide' and 'protein' bank In-Reply-To: <001901c66b00$7bf9d360$bff0a18d@georgetown.mei.georgetown.edu> Message-ID: <033d01c66b19$e4eba240$2f01a8c0@GOLHARMOBILE1> I'm willing to bet it's a bug in IE 7. Its still in beta, so I doubt NCBI will do anything about it until IE 7 is oficially released, but you might want to email the NCBI helpdesk anyway... -----Original Message----- From: Natarajan Ganesan [mailto:natarajanganesan at gmail.com] Sent: Friday, April 28, 2006 4:15 PM To: golharam at umdnj.edu; 'The general forum at Bioinformatics.Org' Subject: RE: [BiO BB] Re: Latest Internet explorer 7.0 doesnt support"LINK"outtool in NCBI's 'nucleotide' and 'protein' bank Importance: High Yes, it does. I checked it. Natarajan -----Original Message----- From: bio_bulletin_board-bounces+natarajanganesan=gmail.com at bioinformatics.org [mailto:bio_bulletin_board-bounces+natarajanganesan=gmail.com at bioinforma tics .org] On Behalf Of Ryan Golhar Sent: Friday, April 28, 2006 3:07 PM To: 'The general forum at Bioinformatics.Org' Subject: RE: [BiO BB] Re: Latest Internet explorer 7.0 doesnt support"LINK"outtool in NCBI's 'nucleotide' and 'protein' bank Does it work with Firefox/Mozilla? -----Original Message----- From: bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org [mailto:bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org ] On Behalf Of Natarajan Ganesan Sent: Friday, April 28, 2006 2:53 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Re: Latest Internet explorer 7.0 doesnt support "LINK"outtool in NCBI's 'nucleotide' and 'protein' bank Importance: High This message is for those who are familiar with using the 'Links' facility when searching for 'nucleotide' OR 'protein' sequences. Normally one sees a popup that links the particular result across a panel of NCBI services. This worked well in IE6.0. However the latest IE7.0 beta seems to have an error that prevents this popup. I believe this will be soon rectified by the NCBI, but till then sticking with IE6.0 is good. Natarajan Ganesan Email: ng6 at georgetown.edu Homepage: http://www.georgetown.edu/faculty/ng6/ -----Original Message----- From: J.W. Bizzaro [mailto:jeff at bioinformatics.org] Sent: Friday, April 28, 2006 12:39 PM To: ng6 at georgetown.edu Subject: Re: Latest Internet explorer 7.0 doesnt support "LINK"out tool in 'nucleotide' and 'protein' bank Hi Natarajan, You might want to post this to the BiO Bulletin Board instead: bbb at bioinformatics.org Thanks, Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From hamid at ibb.ut.ac.ir Sat Apr 29 01:24:15 2006 From: hamid at ibb.ut.ac.ir (hamid) Date: Sat, 29 Apr 2006 09:54:15 +0430 Subject: [BiO BB] Finding (Predicting) a Proein family in a new organism using only Bioinformatics approach Message-ID: Hi buddy, I have a question regarding to find a new protein family in a new organism. Suppose we have the whole proteome of organism "O", although we have 200 proteins regarding to protein family "F" those belongs to several subunits of complete system "S". We doubt whether there is system "S" in organism "O" or not. I have done a multiple alignment among whole proteome of "O" (almost 1200 proteins) and all the proteins belonging to "F" acheieved from several organisms those are proven to have system "S" in them. I achieved a huge alignment file. Now I do not know how can I find that are there any proteins in "O" proteome relating to "F" family. Please guide me in this regard. Yours Behnam /* Hamid( Behnam )Nikbakht, M.Sc of Cell and Molecular Sciences Bioinformatics Center Laboratory of Biophysics and Molecular Biology Institute of Biochemistry and Biophysics University of Tehran P.O.Box 13145-1384 Tehran, Iran. Tel: (+98 21) 664-98672 Fax: (+98 21) 669-56985 Alt. E-Mail : hamid at ibb.ut.ac.ir */ -------------- next part -------------- An HTML attachment was scrubbed... URL: From boris.steipe at utoronto.ca Sat Apr 29 09:35:33 2006 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Sat, 29 Apr 2006 09:35:33 -0400 Subject: [BiO BB] Finding (Predicting) a Proein family in a new organism using only Bioinformatics approach In-Reply-To: References: Message-ID: <0F9D6D3C-1AEA-48F9-A406-47366D9B58DE@utoronto.ca> Let me rephrase your question so I can be sure I understand it: You are looking for evidence for the presence of a certain system (pathway?) in an organism. You know the components of that system in another organism. I am not sure why you would do a multiple alignment for this task. What you are looking for is the presence or absence of particular genes - multiple alignments are useful to compare genes, not to search them. Surely you have not strung the whole proteome into a string and then tried to align that? That approach must fail because you would be trying to align similar fragments with shuffled order. The correct approach is to generate a phylogenetic profile. (1) To begin with, you need a set of reference sequences that are components of your system S. I assume you can take that from literature references. Then, for several proteomes for which know that they contain your system S, you compare all sequences with each of your reference sequences (by BLAST, FASTA, or, if you have the computational resources, by full dynamic alignment (EMBOSS program "Needle")). For each reference sequence, you note whether it has an orthologue in the proteome you are analysing (using the common definition of "reciprocal best matching pairs" to find orthologues). The result is a profile that represents a system component in every column, an organism in every row, and a yes/no information in every cell, that describes whether an orthologue is present or absent. In this first step you establish that your idea of the reference set is indeed correct in the sense that the components from your reference list really have orthologues in (nearly) all organisms that you believe have that system. (2) next you need to understand how the absence of your system affects a proteome. You do the same analysis, but this time with organisms for which you know that the system S is absent. As a result you will understand which components are affected by the presence or absence of the system you are looking for. (3) Finally, you do the analysis with your query organism. It is likely going to be obvious which class this proteome belongs to. Searching for "phylogenetic profiles" in PubMed will give you some background reading, in particular http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15901854 seems to me to discuss something similar to what you want to do... ... unless I have misunderstood your question, then you'll just have to spend more time explaining it clearly :-) Hope this helps, Boris On 29 Apr 2006, at 01:24, hamid wrote: > Hi buddy, > I have a question regarding to find a new protein family in a new > organism. > Suppose we have the whole proteome of organism "O", although we > have 200 proteins regarding to protein family "F" those belongs to > several subunits of complete system "S". We doubt whether there is > system "S" in organism "O" or not. I have done a multiple alignment > among whole proteome of "O" (almost 1200 proteins) and all the > proteins belonging to "F" acheieved from several organisms those > are proven to have system "S" in them. I achieved a huge alignment > file. Now I do not know how can I find that are there any proteins > in "O" proteome relating to "F" family. > Please guide me in this regard. > Yours > Behnam > > /* > Hamid( Behnam )Nikbakht, > M.Sc of Cell and Molecular Sciences > Bioinformatics Center > Laboratory of Biophysics and Molecular Biology > Institute of Biochemistry and Biophysics > University of Tehran > P.O.Box 13145-1384 > Tehran, Iran. > Tel: (+98 21) 664-98672 > Fax: (+98 21) 669-56985 > Alt. E-Mail : hamid at ibb.ut.ac.ir > */ > > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From crishnakh at gmail.com Sat Apr 29 10:51:25 2006 From: crishnakh at gmail.com (Francisco G.P.) Date: Sat, 29 Apr 2006 16:51:25 +0200 Subject: [BiO BB] Re: Latest Internet explorer 7.0 doesnt support "LINK"out tool in, 'nucleotide' and 'protein' bank In-Reply-To: <20060429144007.9FCBB214268@primary.bioinformatics.org> References: <20060429144007.9FCBB214268@primary.bioinformatics.org> Message-ID: <44537D6D.5040603@gmail.com> Why do you use IE? Firefox/mozilla is better than IE, and free From skwofie at mail.biotech.uwc.ac.za Sun Apr 30 13:09:32 2006 From: skwofie at mail.biotech.uwc.ac.za (skwofie at mail.biotech.uwc.ac.za) Date: Sun, 30 Apr 2006 19:09:32 +0200 (SAST) Subject: [BiO BB] The First African Structural Biology Conference Message-ID: <49460.172.16.20.21.1146416972.squirrel@www.biotechnology.uwc.ac.za> The First African Structural Biology Conference Macromolecular Structure, Health and Biotechnology in Developing Countries The Wilderness, South Africa 24-27 October 2006 The First African Structural Biology (FASB) conference will be held in The Wilderness, South Africa. The conference will focus on the contributions and potential contributions of Structural Biology to the development of science and the creation of wealth in Africa with some emphasis on biotechnology and the alleviation of the disease burden of Africa. In particular, the conference has the following aims: 1. To promote structural biology in Africa, particularly in South Africa 2. To discuss contributions to the relief of disease, especially, TB, AIDS and malaria that have been made through an understanding of macromolecular structure 3. To provide the opportunity for South African students and scientists to meet and interact with some of the leading Structural Biologists in several fields that are relevant to our continent 4. To explore the merit and practicality of studying macromolecular structure in Africa 5. To discuss strategic and funding policies for structural biology and benchmark South Africa against other developing countries, notably Brazil and India 6. To identify projects of interest to the South African community in which structural analysis could play a role. The early registration deadline is 1 May 2006. Abstracts are due on 31 August 2006 Expression of interest and registration forms can be submitted online by visiting our website: http://sbio.uct.ac.za/conference Plenary lecturers: Tom Blundell (http://www-cryst.bioc.cam.ac.uk/~tom/) M. Vijayan (http://mbu.iisc.ernet.in/~mv/ ) Ed Egelman (http://www.people.virginia.edu/~ehe2n/) Peter Kwong (http://www.niaid.nih.gov/vrc/labs_kwong.htm) Joachim Frank (http://www.wadsworth.org/resnres/bios/frank.htm) Helen Saibil (http://people.cryst.bbk.ac.uk/~ubcg16z/) Igor Polikarpovhttp://www.if.sc.usp.br/pessoal/Gera_PadraoProf.msql?cod_obj=1178) Iain Campbell (http://www.ocms.ox.ac.uk/idc/) Gert Vriend (http://swift.cmbi.ru.nl/gv/) David Rice (http://www.shef.ac.uk/mbb/academic/staff/rice.html) James A. Sacchettini (http://puffer.tamu.edu/) Andreas Hoenger http://www.embl-heidelberg.de/ExternalInfo/hoenger/Hoenger_index.html) Krishna Murthy (http://main.uab.edu/show.asp?durki=34977) Ravi Acharya (http://www.bath.ac.uk/~bsssi/cgi/ravi_main.pl) Karolin Luger http://www.bmb.colostate.edu/faculty_detailed.cfm?lastname=Luger&firstname=K) Steve Bryant http://www.ncbi.nlm.nih.gov/Structure/RESEARCH/res.shtml) Christian Sommerhoff (http://webinfo.campus.lmu.de/view_person.cfm?ps=27095&cl=12) Conference Organizer: Trevor Sewell Institute of Infectious Disease and Molecular Medicine Wolfson Pavilion, Level 3 Faculty of Health Sciences University of Cape Town Anzio Road Observatory, 7925 South Africa Tel.: +27-21-6502817 Fax: +27-21-6891528 E-mail: sewell at uctvms.uct.ac.za Conference Organizing Committee: Dr Arvind Varsani (arwind at science.uct.ac.za) Professor Girish Kotwal (gkotwal at curie.uct.ac.za) Professor Ed Sturrock (sturrock at curie.uct.ac.za) Dr Muhammed Sayed (msayed at uwc.ac.za) Dr David Pugh (dpugh at uwc.ac.za) Miss Eulashini Chuntharpursat (eulashini at uctbc1.uct.ac.za) Mrs Miranda Waldron (mwaldron at uctvms.uct.ac.za) Miranda Waldron, Electron Microscope Unit, University of Cape Town, South Africa Tel +944 (0)21 650 2818 Fax +944 (0)21 689 1528 From nagesh.chakka at anu.edu.au Tue Apr 25 03:37:09 2006 From: nagesh.chakka at anu.edu.au (Nagesh Chakka) Date: Tue, 25 Apr 2006 17:37:09 +1000 Subject: [BiO BB] Fish genomics Message-ID: <444DD1A5.20801@anu.edu.au> Hi All, I just started work with fish genomes for my comparative study. I am a bit puzzled as to why three different fish species were selected for sequencing (Danio rerio , Fugu rubripes, and Tetraodon nigroviridis). Is there is any advantage in each of these species selected for sequencing which is not there in the other? I am addressing this question to this forum as I have a feeling that someone out there may be working with fish genome and may be having extensive information about what I was looking for. Please also note that I could not find any straight forward answer to my question searching the web. Thanks Nagesh