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[gofriends] Automatic Gene Ontology Annotation Tools

I. Friedberg idoerg at gmail.com
Mon May 21 08:50:00 PDT 2007


My corrections to the JAFA listing:

NR: 10
>  Name: JAFA
> Paper: Iddo Friedberg, Tim Harder and Adam Godzik JAFA: a Protein Function
Annotation Meta Server Nucleic Acids Res. 2006 Jul 1;34(Web Server
issue):W379-81
> 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: YES
> GO graph visualisation: YES
> Available: web interface
> Description: Joined Assembly of Function Annotations (InterProScan,
> GOtcha, GoFigure, Goblet, Phydbac)
> Link: http://jafa.burnham.org

And adding PFP:

> Name: PFP
> Paper: Hawkins t, Luban S and Kihara D Enhanced automated function
prediction using distantly related sequences and contextual association by
PFP Protein Sci. 2006 Jun;15(6):1550-6

> High-throughput: one at a time
> Input Data: only proteins, fasta
> Method: PSI-BLAST with a Function Associated matrix
> Annotation types: GO
> Evidence Codes: no
> Manual GO curation: no
> GO tree visualisation: no
> GO graph visualisation: no
> Available: web interface
> Description: PSI BLAST coupled with curated associateion matrices to
increase sensitivity and specificity of predictions.
> Link: http://dragon.bio.purdue.edu/pfp/index.html



-- 

I. Friedberg

"The only problem with troubleshooting is that
sometimes trouble shoots back."
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