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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,
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.
