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[gofriends] Automatic Gene Ontology Annotation Tools

Ana Conesa aconesa at cipf.es
Mon May 28 01:45:24 PDT 2007


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Hi Chris

I think that the development of a MAIGOT or any protocol for recording
metadata on GO tools is very interesting, but not only for having a
standardized way to describe GO tool but specially with the idea of
providing in the end a resource where people could search for tools
having specific functionalities. The number and diversity of GO tools is
very large already and many of them have features that go beyond to what
could fit in a simple 3 category system -such as now- or which can be
well described in a short description. We will love to participate in
that elaboration.

I also want to clarify that our question to the list on Automatic
Annotation Tools was not with the aim of creating an own catalog but
simply to complete "Table 1" in the manuscript we are preparing at the
moment... we really do not want to maintain a listing of tools!!!

Cheers,
Ana





Stefan Goetz wrote:
> Hi Chis, 
> sure, I think that's a very good idea to present the tools
> characteristics based on a metadata model and list of tags. Would help
> to clear a lot of peoples doubts on which tool actually to use. I would
> be happy to contribute in any way. 
> Did you think than about any kind of userfreindly search interface to
> obtain, for example, what I was searching for: a lis of tools only for
> automatic functional annotation?
> Cheers, Stefan     
> 
> 
>> -----Original Message-----
>> From: Chris Mungall [mailto:cjm at fruitfly.org] 
>> Sent: Thursday, May 24, 2007 3:47 AM
>> To: sgoetz at cipf.es
>> Cc: Eurie Hong; Jane Lomax; Amelia Ireland; Seth Carbon
>> Subject: Re: [gofriends] Automatic Gene Ontology Annotation Tools
>>
>>
>> Hi Stefan
>>
>> I don't know if you know but we maintain a list of tools here:
>> http://www.geneontology.org/GO.tools.shtml
>>
>> as it happens we are just in the process of re-engineering this from  
>> a collection to web pages into metadata that can be used to generate  
>> nice html.
>>
>> we are more than happy for you to also have your own list of tools,  
>> but perhaps it would be easier for us and for the community if we  
>> collaborated on maintaining the core tool metadata. We could each  
>> present the metadata in our own way. We would have some protocol to  
>> avoid forcing people to submit one set of metadata to us and another  
>> to you. Would you agree?
>>
>> If so, then the first thing we should decide is the minimal  
>> information about a GO tool (MIAGOT?). This would be a simple but  
>> extensible list of tags, essentially the union of what you 
>> have below  
>> and the info we currently maintain.
>>
>> Cheers
>> Chris
>>
>> On May 18, 2007, at 8:16 AM, Stefan Goetz wrote:
>>
>>> Hi All,
>>> we are trying to make an up-to-date list of all the 
>> working, free and
>>> public available tools who are able to generate or predict  
>>> automatically
>>> (not only  recover) gene ontology annotations based on (novel)  
>>> sequence
>>> data. We made a first listing and would like to invite you all to
>>> discuss, complete or correct this list. Thanks in advanced for your
>>> contributions and help.
>>> Regards,
>>> Stefan Goetz
>>>
>>>
>>> Automatic Gene Ontology Annotation Tools
>>> (alphabetical order)
>>>
>>> NR: 1
>>> Name: AutoFact
>>> Paper: BMC BioInformatics, 2005
>>> High-throughput: yes
>>> Input Data: fasta
>>> Method: sequences are classified into 6 different annotation  
>>> categories,
>>> blast-based
>>> Evidence Codes: no
>>> Manual GO curation: GO, COG, KEGG, Locus, ?
>>> GO tree visualisation: no
>>> GO graph visualisation: no
>>> Avalible: Perl implementation online
>>> Description: An Automatic Functional Annotation and Classification  
>>> Tool
>>> Link: http://www.bch.umontreal.ca/Software/AutoFACT.htm
>>>
>>> NR: 2
>>> Name: Blast2GO
>>> Paper: Bioinformatics. 2005 Sep
>>> High-throughput: yes (arround 30 000 Seqs, memory dependent)
>>> Input Data: fasta, blast-xml
>>> Method: combination of similarity search based (blast), domain based
>>> (interproscan) and datamining based (annex) annotation
>>> Annotation types: GO, InterPro, Kegg
>>> Evidence Codes: yes
>>> Manual GO curation: yes
>>> GO tree visualisation: no
>>> GO graph visualisation: yes
>>> Avalible: java web start + web service
>>> Description: A universal Gene Ontology annotation, visualization and
>>> analysis tool for functional genomics research
>>> Link: http://www.blast2go.org
>>>
>>> NR: 3
>>> Name: GOanna/AgBase
>>> Paper: BMC Genomics
>>> High-throughput: file upload (size limit?), (user gets notified by  
>>> email
>>> when data is ready)
>>> Input Data: fasta
>>> Method: Top-Blast
>>> Annotation types: GO, ?
>>> Evidence Codes: yes
>>> Manual GO curation: no
>>> GO tree visualisation: -
>>> GO graph visualisation: -
>>> Avalible: webinterface
>>> Description: GOanna is used to find annotations for proteins using
>>> similarity search. The resulting file contains GO annotations of  
>>> the top
>>> BLAST hits. The sequence alignments are also provided so 
>> the user can
>>> use these to access the quality of the match.
>>> Link: http://agbase.msstate.edu/GOAnna.html
>>>
>>> NR: 4
>>> Name: GOAnno
>>> Paper: Bioinformatics. 2005 May
>>> High-throughput: one at a time
>>> Input Data: only proteins, fasta
>>> Method: evolutionary information in multible alignments organized
>>> herarchically into functional subfamilies
>>> Annotation types: GO, ?
>>> Evidence Codes: no
>>> Manual GO curation: no
>>> GO tree visualisation: -
>>> GO graph visualisation: -
>>> Avalible: webinterface
>>> Description: GO annotation based on multiple alignment
>>> Link: http://bips.u-strasbg.fr/GOAnno/
>>>
>>> NR: 5
>>> Name: GOblet
>>> Paper: Two NAR papers, 2003,2004
>>> High-throughput: max ~150 seqs
>>> Input Data: fasta
>>> Method: all-hits mapping with probability scoring	
>>> Annotation types: GO
>>> Evidence Codes: no
>>> Manual GO curation: no
>>> GO tree visualisation: yes
>>> GO graph visualisation: no
>>> Avalible: webinterface, output in java applet
>>> Description: A platform for Gene Ontology annotation of anonymous
>>> sequence data
>>> Link: http://goblet.molgen.mpg.de
>>>
>>> NR: 6
>>> Name:GoFigure + GoDel
>>> Paper: Bioinformatics. 2003 Dec
>>> High-throughput: one at a time
>>> Input Data: fasta
>>> Method: GoFigure (mappping of GO terms to Blast Hits) + GODel  
>>> (Selection
>>> of terms by eValue and evicdence codes)
>>> Annotation types: GO
>>> Evidence Codes: yes
>>> Manual GO curation: no
>>> GO tree visualisation: no
>>> GO graph visualisation: yes
>>> Avalible: webinterface
>>> Description: BLAST to predict Gene Ontology annotation
>>> Link: http://udgenome.ags.udel.edu/gofigure/
>>>
>>> NR: 7
>>> Name: GOtcha
>>> Paper: no publication
>>> High-throughput: one at a time
>>> Input Data: fasta?
>>> Method: all-hits mapping with probability scoring
>>> Annotation types: GO
>>> Evidence Codes: yes
>>> Manual GO curation: no
>>> GO tree visualisation: yes
>>> GO graph visualisation: no
>>> Avalible: webinterface
>>> Description: GOtcha uses sequence similarity searches to 
>> associate GO
>>> terms with your sequence. These are ranked by probability and  
>>> displayed
>>> graphically on a subtree of Gene Ontology. You will need an 
>> up to date
>>> browser and JavaScript to get the best from the results.
>>> Link: http://www.compbio.dundee.ac.uk/gotcha/gotcha.php
>>>
>>> NR: 8
>>> Name: HT-GO-FAT
>>> Paper: no publication
>>> High-throughput: yes
>>> Input Data: -
>>> Method: sequence similarity (custom blast db)
>>> Annotation types: GO, ?
>>> Evidence Codes: no
>>> Manual GO curation: ?
>>> GO tree visualisation: ?
>>> GO graph visualisation: ?
>>> Avalible: Windows .NET (download after request)
>>> Description: High Throughput Gene Ontology Functional Annotation  
>>> Toolkit
>>> (Ht-Go-Fat) Utilized for Animal and Plant
>>> Link: http://genome4.ars.usda.gov/farm/dload.php
>>>
>>> NR: 9
>>> Name: InterProScan
>>> Paper: Nucleic Acids Res. 2007
>>> High-throughput:  max. 10 Seqs (web interface)
>>> Input Data: fasta
>>> Method: GOs through domains
>>> Annotation types: GO, ?
>>> Evidence Codes: no
>>> Manual GO curation: no
>>> GO tree visualisation: no
>>> GO graph visualisation: no
>>> Avalible: webinterface, web service
>>> Description: Domain searches agains: BlastProDom, 
>> FPrintScan, HMMPIR,
>>> HMMPfam, HMMSmart, HMMTigr, ProfileScan, ScanRegExp, SuperFamily,
>>> SignalPHMM, TMHMM, HMMPanther, Gene3D	
>>> Link: http://www.ebi.ac.uk/InterProScan/
>>>
>>> NR: 10
>>> Name: JAFA
>>> Paper: no publication
>>> High-throughput: one at a time
>>> Input Data: only proteins, fasta
>>> Method: Joined Assembly of Function Annotations (InterProScan,
>>> GOtcha,GoFigure, Goblet, Phydbac)
>>> Annotation types: GO
>>> Evidence Codes: yes/no
>>> Manual GO curation: no
>>> GO tree visualisation: no
>>> GO graph visualisation: no
>>> Avalible: webinterface
>>> Description: Joined Assembly of Function Annotations (InterProScan,
>>> GOtcha, GoFigure, Goblet, Phydbac)
>>> Link: http://jafa.burnham.org
>>>
>>> NR: 11
>>> Name: OntoBlast
>>> Paper: Nucleic Acids Res. 2003
>>> High-throughput: one at a time
>>> Input Data: only protein, fasta
>>> Method: sequence similarities
>>> Annotation types: GO
>>> Evidence Codes: no
>>> Manual GO curation: no
>>> GO tree visualisation: no
>>> GO graph visualisation: no
>>> Avalible: webinterface
>>> Description: OntoBlast function: From sequence similarities  
>>> directly to
>>> potential functional annotations by ontology terms
>>> Link: http://functionalgenomics.de/ontogate/
>>>
>>>
>>> NR: 12
>>> CompuGen?
>>>
>>> NR: 13
>>> GOA?
>>>
>>> NR: 13
>>> GOAT?
>>>
>>> NR: 14
>>> est2uni?
>>>
>>>
>>> ...
>>>
>>>
>>>
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