FunSimMat - Functional Similarity Matrix

FunSimMat is a comprehensive resource of semantic and functional similarity values. It allows searching for functional similarity values for proteins
(extracted from UniProt), and protein families (Pfam, SMART). FunSimMat provides several different semantic and functional similarity measures
for each protein pair using the Gene Ontology annotation from UniProtKB.
There are several search options available:

Semantic similarity:

For a list of GO terms, FunSimMat performs an all-against-all comparison and displays the semantic similarity values.

Functional similarity:

Compare one protein / protein family to a list of proteins / protein families
Compare a list of GO terms to a list of proteins / protein families

Help page

News

November 18, 2009: A paper describing new features in FunSimMat has been published in Nucleic Acids Research.
You can find it here.
August 6, 2009: We resolved an issue with the XML-RPC server. If you experience any further problems, please contact us at funsimmat [at] mpi-inf [dot] mpg [dot] de.
We are sorry for any inconveniences caused.
June 24, 2009: FunSimMat release 3.1 is online.
The current release was built using UniProKB 15.3, GOA release May 2009, Pfam 23, SMART from InterPro release 20, and OMIM (June 10, 2009).
See the release notes for more details.

Query FunSimMat

The query form can be found here.

Reference

Schlicker A., Albrecht M.
FunSimMat update: new features for exploring functional similarity.
Nucleic Acids Research, 2010, 38(Database issue). doi: 10.1093/nar/gkm979. Paper
Schlicker A., Albrecht M.
FunSimMat: a comprehensive functional similarity database.
Nucleic Acids Research, 2008, 36(Database issue):D434-439. doi: 10.1093/nar/gkm806. Paper

Contact

If you have any questions, comments, suggestions, criticism, or encounter any problem with the web server feel free to contact us at: funsimmat [at] mpi-inf [dot] mpg [dot] de.