[BiO BB] RE:

[Boris Steipe]

Venkata Satagopam wrote:
> 
> Yes, you can get the full entry of GenBank
> from any public SRS servers. Here is the
> link where you can found many public SRS
> servers..
> http://www.lionbio.co.uk/publicsrs.html
> 
> OR you can look at http://igbmc.u-strasbg.fr/srs6/
> 
> regards
> venkata

Yes, that too ... but SeqHound is open source, unlimited use, whereas your
company markets SRS for profit under restricted terms od use.


SeqHound: Licesne: GPL <http://www.gnu.org/copyleft/gpl.html>
SRS terms of use : <http://iubio.bio.indiana.edu/srs/SRStermsofuse.html>


Respectfully,

Boris
========================================
> 
> -----Original Message-----
> From:
> Posted At: Tuesday, January 01, 1991 1:00 AM
> Posted To: Inbox
> Conversation:
> Subject:
> 
> When replying, PLEASE edit your Subject line so it is more specific
> than "Re: BiO_Bulletin_Board digest, Vol..."  And, PLEASE delete any
> unrelated text from the body.
> 
> Today's Topics:
> 
>    1. Re: Is it possible to Blast against genBank files (jordan swanson)
>    2. Re: Is it possible to Blast against genBank files (Iddo Friedberg)
>    3. Re: Is it possible to Blast against genBank files (Boris Steipe)
> 
> --__--__--
> 
> Message: 1
> Date: Thu, 18 Dec 2003 12:53:51 -0800 (PST)
> From: jordan swanson <jordanmswanson at yahoo.com>
> Subject: Re: [BiO BB] Is it possible to Blast against genBank files
> To: bio_bulletin_board at bioinformatics.org
> Reply-To: bio_bulletin_board at bioinformatics.org
> 
> > You mean that the BLAST results only have the Fasta
> > file annotation in
> > them. Well, AFAIK, the only input to formatdb is
> > Fasta or ASN.1. The
> > output, anyhow, would be a one-liner.
> >
> > How about giving her the output in HTML (-T option)?
> > blast automatically
> > builds a link from each hit to the NCBI page. So
> > using a browser, your
> > coworker can skim the one-line annotation, and then
> > click & delve into
> > the more interesting ones.
> 
> We did try that, however with the large number of
> sequences she needed to look up, she was black-listed
> from their machine.  We need to find the full GenBank
> entry given a particular identifier, unfortunately the
> easiest way I've found so far seems to be the Entrez
> system, and that appears to not be possible to
> download.  Is there another way to get the full
> genbank entry given the identifier?
> 
> ---
> Jordan Swanson
> 
> __________________________________
> Do you Yahoo!?
> New Yahoo! Photos - easier uploading and sharing.
> http://photos.yahoo.com/
> 
> --__--__--
> 
> Message: 2
> Date: Thu, 18 Dec 2003 13:00:25 -0800
> From: Iddo Friedberg <idoerg at burnham.org>
> To: bio_bulletin_board at bioinformatics.org
> Subject: Re: [BiO BB] Is it possible to Blast against genBank files
> Reply-To: bio_bulletin_board at bioinformatics.org
> 
> Biopython has something that can do that. Maybe Bioperl too. Let me know
> if you want the Python code.
> 
> ./I
> 
> jordan swanson wrote:
> >>You mean that the BLAST results only have the Fasta
> >>file annotation in
> >>them. Well, AFAIK, the only input to formatdb is
> >>Fasta or ASN.1. The
> >>output, anyhow, would be a one-liner.
> >>
> >>How about giving her the output in HTML (-T option)?
> >>blast automatically
> >>builds a link from each hit to the NCBI page. So
> >>using a browser, your
> >>coworker can skim the one-line annotation, and then
> >>click & delve into
> >>the more interesting ones.
> >
> >
> > We did try that, however with the large number of
> > sequences she needed to look up, she was black-listed
> > from their machine.  We need to find the full GenBank
> > entry given a particular identifier, unfortunately the
> > easiest way I've found so far seems to be the Entrez
> > system, and that appears to not be possible to
> > download.  Is there another way to get the full
> > genbank entry given the identifier?
> >
> > ---
> > Jordan Swanson
> >
> > __________________________________
> > Do you Yahoo!?
> > New Yahoo! Photos - easier uploading and sharing.
> > http://photos.yahoo.com/
> > _______________________________________________
> > BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> >
> >
> 
> --
> Iddo Friedberg, Ph.D.
> The Burnham Institute
> 10901 N. Torrey Pines Rd.
> La Jolla, CA 92037
> USA
> Tel: +1 (858) 646 3100 x3516
> Fax: +1 (858) 646 3171
> http://ffas.ljcrf.edu/~iddo
> 
> --__--__--
> 
> Message: 3
> Date: Thu, 18 Dec 2003 17:01:20 -0500
> From: Boris Steipe <boris.steipe at utoronto.ca>
> To: bio_bulletin_board at bioinformatics.org
> Subject: Re: [BiO BB] Is it possible to Blast against genBank files
> Reply-To: bio_bulletin_board at bioinformatics.org
> 
> jordan swanson wrote:
> >
> > > You mean that the BLAST results only have the Fasta
> > > file annotation in
> > > them. Well, AFAIK, the only input to formatdb is
> > > Fasta or ASN.1. The
> > > output, anyhow, would be a one-liner.
> > >
> > > How about giving her the output in HTML (-T option)?
> > > blast automatically
> > > builds a link from each hit to the NCBI page. So
> > > using a browser, your
> > > coworker can skim the one-line annotation, and then
> > > click & delve into
> > > the more interesting ones.
> >
> > We did try that, however with the large number of
> > sequences she needed to look up, she was black-listed
> > from their machine.  We need to find the full GenBank
> > entry given a particular identifier, unfortunately the
> > easiest way I've found so far seems to be the Entrez
> > system, and that appears to not be possible to
> > download.  Is there another way to get the full
> > genbank entry given the identifier?
> >
> > ---
> > Jordan Swanson
> 
> Yes, you can get the files through the SeqHound remote Perl API - easy to
> program and no blacklists.
> 
> See:            <http://blueprint.org/seqhound/seqhound.html>
> and especially: <http://blueprint.org/seqhound/api_help/apifunctslist.html>
> 
> Best regards,
> 
> Boris
> 
> ---
> Boris Steipe
> University of Toronto
> Program in Proteomics & Bioinformatics
> Departments of Biochemistry & Molecular and Medical Genetics
> http://biochemistry.utoronto.ca/steipe
> 
> --__--__--
> 
> _______________________________________________
> BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> 
> End of BiO_Bulletin_Board Digest
> =====
> Venkata Pardhasaradhi Satagopam,
> Bioinformatics Scientist,
> Genomics IT Research,
> Office Address  :LION Bioscience AG, Waldhofer Str.98,69123 Heidelberg,GERMANY. Tel: 0049-(0)6221 4038 414
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> 
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