Torsten Waldminghaus: added tags

Torsten Waldminghaus — Mon, 03 Mar 2008 20:43:09 GMT

added tags

←Older revision		Revision as of 20:43, 3 March 2008
Line 120:		Line 120:

	[[Category:Protein]]		[[Category:Protein]]
		+
		+	[[Category:Protocol]]
		+	[[Category:In silico]]
		+	[[Category:Sequence analysis]]

Bill Flanagan at 05:41, 20 November 2007

Bill Flanagan — Tue, 20 Nov 2007 05:41:15 GMT

←Older revision		Revision as of 05:41, 20 November 2007
Line 34:		Line 34:
	== Basic tools ==		== Basic tools ==

-	* [[BLAST]] and [[PSI-BLAST]] <cite>blast psiblast</cite> are commonly used to search for homologous protein sequences by sequence alignment.	+	* [[Wikiomics:BLAST]] and [[Wikiomics:PSI-BLAST]] <cite>blast psiblast</cite> are commonly used to search for homologous protein sequences by sequence alignment.
	* [http://www.expasy.org/prosite/ Prosite] <cite>prosite_first prosite_last</cite> is a searchable database of sequence patterns that are associated with some biological functions.		* [http://www.expasy.org/prosite/ Prosite] <cite>prosite_first prosite_last</cite> is a searchable database of sequence patterns that are associated with some biological functions.

Line 50:		Line 50:
	* [http://www.ebi.ac.uk/thornton-srv/databases/profunc/ ProFunc] <cite>profunc_a profunc_b</cite> performs predictions from a protein structure		* [http://www.ebi.ac.uk/thornton-srv/databases/profunc/ ProFunc] <cite>profunc_a profunc_b</cite> performs predictions from a protein structure

-	See also [[~~searching~~ for 3D functional sites in a protein structure]].	+	See also [[Wikiomics:Searching for 3D functional sites in a protein structure]].

	Methods using non-sequential sequence features:		Methods using non-sequential sequence features:
Line 71:		Line 71:
	== See also ==		== See also ==

-	* [[Automated function prediction of genes and proteins]], our local community pages	+	* [[Wikiomics:Automated function prediction of genes and proteins]], our local community pages

	* [http://bib.oxfordjournals.org/cgi/content/full/7/3/225?ijkey=n3AzMhAJ4nZjzAy&keytype=ref Automated Function Prediction -- the Genomic Challenge] <cite>afpreview</cite>		* [http://bib.oxfordjournals.org/cgi/content/full/7/3/225?ijkey=n3AzMhAJ4nZjzAy&keytype=ref Automated Function Prediction -- the Genomic Challenge] <cite>afpreview</cite>

Bill Flanagan: 1 revision(s)

Bill Flanagan — Tue, 20 Nov 2007 04:00:46 GMT

1 revision(s)

←Older revision

Revision as of 04:00, 20 November 2007

128.210.48.233: /* References */

128.210.48.233 — Tue, 27 Mar 2007 04:41:54 GMT

References

New page

There are now plenty of proteins which have a totally unknown function. Automated function prediction is an active research field, with a growing community of bioinformaticians as observed at the [http://biofunctionprediction.org AFP-SIG] that took place at the [http://www.iscb.org/ismb2005/ ISMB 2005 conference], and at University of California San Diego in 2006.

Most often, only the sequence of the protein is known, but there are also hundreds of protein structures of unknown function which are provided by the [http://en.wikipedia.org/wiki/Structural_genomics structural genomics] centers. Sometimes the proteins come from prokaryotes where the operons make it possible to infer the function of a protein from its genomic context, but this is more complicated in eukaryotes. And more generally, it is easier to guess right when a given protein has well-described homologs than when it belongs to a family of unknown biological role.

Of course, the notion of ''protein function'' is pretty broad and cannot easily be encoded without relying on a complex vocabulary. For that matter, the [http://www.geneontology.org/ Gene Ontology] aka GO provides hierarchical set of keywords called GO terms which describe different aspects of protein function with different levels of precision. GO is currently imposing itself as a standard for proteome annotation and function prediction of proteins.

Among the current software tools that exist today, several main strategies can be distinguished:
* homology search and transfer of annotations:
** sequence alignment
** structure alignment
* function inference by genomic context
* phylogenomic approaches
* prediction from structure using similarities that are not homology-based:
** local sequence patterns
** physico-chemical sequence features
** 3D local sites
** 3D physico-chemical features

== Servers which competed at the AFP-SIG 2005 ==

See also the short summaries by the authors themselves at [http://ffas.burnham.org/AFP/Challenge/servers/ the official site of AFP-SIG 2005].

These servers are based on transfer of function based on homology:
* [http://www.salilab.org/~marcius/beta_dbali/?page=tools&action=f_chain_all DBAli Annolite] <cite>dbali</cite>
* [http://dragon.bio.purdue.edu/pfp/pfp.html PFP]<cite> pfp </cite>
* [http://www.cs.ualberta.ca/~bioinfo/PA/ ProteomeAnalyst] <cite>pa pa-gosub</cite>
* [http://genius.embnet.dkfz-heidelberg.de/menu/biounit/open-husar GOPET] <cite>gopet</cite>

And the other servers are:
* [http://www.ebi.ac.uk/interpro/internal-tools/squid-internal/squid-srv/aaSpearmintTools.do SpearMint] and [http://www.ebi.ac.uk/interpro/internal-tools/squid-internal/squid-srv/aaRulebaseTools.do RuleBase] (not public yet) <cite>wieser2004</cite>
* [http://igs-server.cnrs-mrs.fr/phydbac/indexPS.html PhydBac] <cite>enault2003 phydbac phydbac2 fusiondb phydbac2005</cite> analyzes bacterial proteins using genomic context.
* [http://www.doe-mbi.ucla.edu/Services/ProKnow/ ProKnow] <cite>proknow</cite> searches for known 3D folds, sequences, motifs, and functional linkages

== Basic tools ==

* [[BLAST]] and [[PSI-BLAST]] <cite>blast psiblast</cite> are commonly used to search for homologous protein sequences by sequence alignment.
* [http://www.expasy.org/prosite/ Prosite] <cite>prosite_first prosite_last</cite> is a searchable database of sequence patterns that are associated with some biological functions.

== Other protein function prediction servers ==

[http://jafa.burnham.org/ JAFA] is a meta-server for function prediction of proteins: it produces a prediction based on an aggregate from other servers. You might want to start with [http://jafa.burnham.org/ JAFA] since it queries [http://jafa.burnham.org/learnMore.html 5 servers] (GOFigure,
GOblet,
InterproScan,
GOtcha,
PhydBac) and shows you where their results agree and differ.

Miscellaneous servers:
* [http://wolf.bms.umist.ac.uk/~mjfikpd2/predict/enon.html Protein Function Prediction Server] - Protein function predictions from PDB structures <cite>dobson-doig</cite>. An enzyme/non-enzyme predictor, and an enzyme class predictor are available.
* [http://udgenome.ags.udel.edu/gofigure/ GoFigure] <cite>gofigure</cite> predicts the function of a gene or protein
* [http://www.ebi.ac.uk/thornton-srv/databases/profunc/ ProFunc] <cite>profunc_a profunc_b</cite> performs predictions from a protein structure

See also [[searching for 3D functional sites in a protein structure]].

Methods using non-sequential sequence features:
* [http://www.cbs.dtu.dk/services/ProtFun/ ProtFun] <cite>protfun2002 protfun2003</cite>
* [http://abcis.cbs.cnrs.fr/propsearch/propsearch.html PropSearch] <cite>propsearch</cite>

These methods are based on function transfer after homology searches:
* [http://www.blast2go.de Blast2GO] <cite>blast2go</cite>
* [http://functionalgenomics.de/ontogate/ OntoBlast] <cite>ontoblast</cite>
* [http://goblet.molgen.mpg.de/ GOblet] <cite>goblet2003 goblet2004</cite>
* [http://www.compbio.dundee.ac.uk/gotcha/gotcha.php GOtcha] <cite>gotcha</cite>
* Phunctioner <cite>phunctioner</cite> is a method based on the association of GO terms with conserved residues in 3D structural alignments

Phylogenomic approaches:
* [http://orthostrapper.cgb.ki.se/ Orthostrapper] <cite>orthostrapper</cite>
* [http://www.rio.wustl.edu/ RIO] <cite>rio</cite>
* SIFTER <cite>sifter</cite>
* [http://www.up.univ-mrs.fr/evol/figenix/ FIGENIX] <cite>figenix</cite>

== See also ==

* [[Automated function prediction of genes and proteins]], our local community pages

* [http://bib.oxfordjournals.org/cgi/content/full/7/3/225?ijkey=n3AzMhAJ4nZjzAy&keytype=ref Automated Function Prediction -- the Genomic Challenge] <cite>afpreview</cite>

== References ==
<biblio>
#wieser2004 pmid=15262818
#dbali pmid=11524379
#enault2003 pmid=12855445
#phydbac pmid=12824402
#phydbac2 pmid=15215406
#phydbac2005 pmid=16221304
#fusiondb pmid=14681411
#proknow pmid=15642267
#pa pmid=15215412
#pa-gosub pmid=15608166
#gopet pmid=15333146
#dobson-doig pmid=12850146
#protfun2002 pmid=12079362
#protfun2003 pmid=12651722
#gofigure pmid=14668239
#profunc_a pmid=15980588
#profunc_b pmid=16019027
#ontoblast pmid=12824422
#goblet2003 pmid=12824400
#goblet2004 pmid=15215401
#gotcha pmid=15550167
#orthostrapper pmid=11836216
#rio pmid=12028595
#sifter pmid=16217548
#blast pmid=2231712
#psiblast pmid=9254694
#prosite_first pmid=7584418
#prosite_last pmid=14681377
#phunctioner pmid=15456910
#propsearch pmid=7650738
#figenix pmid=16083500
#blast2go pmid=16081474
#afpreview pmid=16772267
#pfp pmid=16672240
</biblio>

== Credits ==
{{credits}}

* [[User:Martin Jambon|Martin Jambon]]: introduction plus the initial list of tools and papers, put together after the AFP-SIG 2005 conference (at ISMB 2005)
* other Wikiomics authors

[[Category:Protein]]

Wikiomics:Protein function prediction - Revision history

Torsten Waldminghaus: added tags

Bill Flanagan at 05:41, 20 November 2007

Bill Flanagan: 1 revision(s)

128.210.48.233: /* References */