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[gofriends] New functional similarity database - FunSimMat

Andreas Schlicker andreas.schlicker at
Thu Oct 11 23:36:00 PDT 2007

Dear all,

we just published a paper about our new FunSimMat database (Functional Simlarity
Matrix). It provides several precomputed functional similarity measures forall
proteins in UniProtKB, and all Pfam and SMART protein families.

You can find the paper at
and FunSimMat at

Here is the abstract:
Functional similarity based on Gene Ontology (GO) annotation is used in diverse
applications like gene clustering, gene expression data analysis, protein
interaction prediction and evaluation. However, there exists no comprehensive
resource of functional similarity values although such a database would
facilitate the use of functional similarity measures in different applications.
Here, we describe FunSimMat (Functional Similarity Matrix,, a large new database that provides
several different semantic similarity measures for GO terms. It offers various
precomputed functional similarity values for proteins contained in UniProtKB and
for protein families in Pfam and SMART. The web interface allows users to
efficiently perform both semantic similarity searches with GO terms and
functional similarity searches with proteins or protein families. All results
can be downloaded in tab-delimited files for use with other tools. An additional
XML–RPC interface gives automatic online access to FunSimMat for programsand
remote services.

Kind regards,

Andreas Schlicker, M.Sc.
Max-Planck-Institute Informatik
Department 3: Computational Biology and Applied Algorithmics
Campus E1 4
66123 Saarbruecken

Phone: +49 681 9325 321
Fax: +49 681 9325 399

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