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[gofriends] Automatic Gene Ontology Annotation Tools

Stefan Goetz sgoetz at cipf.es
Fri May 18 08:16:32 PDT 2007


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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