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Nucleic Acids Research Advance Access first published online on October 11, 2007
This version published online on November 13, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm806
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

FunSimMat: a comprehensive functional similarity database

Andreas Schlicker* and Mario Albrecht

Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrücken, Germany

*To whom correspondence should be addressed. Tel: +49 681 9325 321; Fax: +49 681 9325 399; Email: andreas.schlicker{at}mpi-inf.mpg.de

Received August 15, 2007. Revised September 13, 2007. Accepted September 17, 2007.

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, http://funsimmat.bioinf.mpi-inf.mpg.de/), 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 programs and remote services.


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