[BiO BB] protein family databases (Interpro)

Dr Nicky Mulder nmulder at science.uct.ac.za
Tue Oct 18 06:26:06 EDT 2005


Dear Andrea

I run the InterPro project and hope I can help with some more information. As
you probably know, all the data is freely available for download, and is
available in xml format. If you are interested in UniProt proteins, all
InterPro matches for these are precaculated and available.
InterPro parent/child relationships are used when some protein signatures are
more sensistive than others and detect subfamilies, or subsets of others. In
this way you can classify a protein on different levels e.g. superfamily,
family and subfamily. PRINTS fingerprints are particularly good at getting
different levels of granularity. The contains/found in relationship is where
you have a signature covering a larger region of sequence and smaller
signatures or domains covering smaller regions within it. This is to show
domain composition.

If you want to run your own sequences through InterProScan, the results are
available in several formats, including html, text and xml.

Let me know if you have any more questions on the data or database.

Nicky


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>    1. protein family databases (Interpro) (Andrea Franceschini)
>    2. Re: protein family databases (Interpro) (Ann Loraine)
>    3. Final CFP: EvoBIO 2006 (Carlos Cotta)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 16 Oct 2005 18:00:31 +0200
> From: "Andrea Franceschini" <atariml at gmail.com>
> Subject: [BiO BB] protein family databases (Interpro)
> To: "biobulletin" <bio_bulletin_board at bioinformatics.org>
> Message-ID: <031f01c5d26a$c16cda70$0801a8c0 at atarippc>
> Content-Type: text/plain; format=flowed; charset="iso-8859-1";
> 	reply-type=original
>
> We are developing a software to automatically retrive some family/domain's
> annotations of a set of proteins.
> In particular we are interested to identify the possible relations between
> the different families.
>
> To accomplish this task we are thinking to use Interpro as source for the
> annotations.
> What do you think about the parent/child  and  contains/found in   relations
> present in Interpro ?
>
> Do you have any suggestion about other databases that we should use ?
> Do you have any suggestion about other possible information that we could
> provide on a particular set of proteins (given us as input by the user)  ?
>
>
> Thankyou very much
> Andrea Franceschini
> University Politecnico of Milan (Italy)
>
>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 16 Oct 2005 19:32:04 -0500
> From: Ann Loraine <aloraine at gmail.com>
> Subject: Re: [BiO BB] protein family databases (Interpro)
> To: "The general forum at Bioinformatics.Org"
> 	<bio_bulletin_board at bioinformatics.org>
> Message-ID:
> 	<83722dde0510161732u2b19bc41hf9b4b36d784524db at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear Andrea,
>
> This service would be of great use to me if it allowed me to transfer
> amino acid sequences directly to your server and get back the results
> directly (instead of via a Web page) in an easy-to-parse format, such
> as XML.
>
> Very best wishes,
>
> Ann Loraine
>
> On 10/16/05, Andrea Franceschini <atariml at gmail.com> wrote:
> > We are developing a software to automatically retrive some family/domain's
> > annotations of a set of proteins.
> > In particular we are interested to identify the possible relations between
> > the different families.
> >
> > To accomplish this task we are thinking to use Interpro as source for the
> > annotations.
> > What do you think about the parent/child  and  contains/found in
> relations
> > present in Interpro ?
> >
> > Do you have any suggestion about other databases that we should use ?
> > Do you have any suggestion about other possible information that we could
> > provide on a particular set of proteins (given us as input by the user)  ?
> >
> >
> > Thankyou very much
> > Andrea Franceschini
> > University Politecnico of Milan (Italy)
> >
> > _______________________________________________
> > Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> >
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 17 Oct 2005 11:30:41 +0200
> From: Carlos Cotta <ccottap at lcc.uma.es>
> Subject: [BiO BB] Final CFP: EvoBIO 2006
> To: bio_bulletin_board at bioinformatics.org
> Message-ID: <5.1.0.14.2.20051017112942.03d85350 at sol10.lcc.uma.es>
> Content-Type: text/plain;	charset=us-ascii;	format=flowed
>
> ----------------------------------------------------------------
>
>                       Final Call for Papers
>
>                           EvoBIO2006
>       Fourth European Workshop on Evolutionary Computation
>             and Machine Learning in Bioinformatics
>                         Budapest, Hungary
>
>            http://evonet.lri.fr/eurogp2006/?page=evobio
>            http://www.cs.vu.nl/~evobio/evobio06.html
>
> ----------------------------------------------------------------
>
> EvoBIO covers research in all aspects of computational intelligence
> in bioinformatics and computational biology. The emphasis is on
> algorithms based on evolutionary computation, on neural networks and
> on other novel optimisation and machine learning methods, that address
> important problems in molecular biology, genomics and genetics, that
> are computationally efficient, and that have been implemented and
> tested in simulations and on real datasets.
>
> The goal of the workshop is to present recent research results,
> including significant work-in-progress, and to identify and explore
> directions of future research, besides stimulating closer interaction
> between members of this scientific community working on bioinformatics.
>
> Each accepted paper will be presented orally at the workshop and
> printed in the proceedings published by Springer in the LNCS series.
> The accepted papers of the first, second, and third edition of EvoBIO
> were published in the Springer Verlag LNCS 2611, 3005, 3449, respectively.
>
> Submission instructions are available at the EvoBIO web pages
> indicated above.
>
> ******  Important Dates ******
>
> Submission deadline: 4 November 2005
> Notification of acceptance:  12 December 2005
> Camera ready papers due: 9 January 2006
> EvoBIO and Evo-events: 10-12 April 2006
>
> ******  General Chairs *******
> Dave Corne, UK
> Elena Marchiori, NL
>
> ******  Program Chairs ******
> Carlos Cotta, Spain
> Jason Moore, USA
>
> ******  Publicity Chair ******
> Jagath C. Rajapakse, Singapore
>
> ******  Program Committee ******
> Jesus Aguilar, Spain
> Wolfgang Banzhaf, Canada
> Jacek Blazewicz, Poland
> David Corne, UK
> Vincenzo Cutello, Italy
> Gary Fogel, USA
> James Foster, USA
> Alex Freitas, UK
> Raul Giraldez, Spain
> Rosalba Giugno, Italy
> Jin-Kao Hao, France
> Natalio Krasnogor, UK
> Bill Langdon, UK
> Bob MacCallum, Sweden
> Elena Marchiori, The Netherlands
> Andrew Martin, UK
> Pablo Moscato, Australia
> Ajit Narayanan, UK
> Vic J. Rayward-Smith, UK
> John Rowe, UK
> Jem Rowland, UK
> El-Ghazali Talbi, France
> Antoine van Kampen, The Netherlands
> Gwen Volkert, UK
> Ray Walshe, Ireland
> Eckart Zitzler, Switzerland
> Igor Zwir, Spain
>
>
>
>
>
> ------------------------------
>
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