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.
Keywords
UniProtSimilarity (geometry)Semantic similarityInterface (matter)Computer scienceCluster analysisAnnotationGene ontologyInformation retrievalXMLBiologyDatabaseComputational biologyData miningBioinformaticsGeneWorld Wide WebArtificial intelligenceGene expressionGenetics
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Publication Info
- Year
- 2007
- Type
- article
- Volume
- 36
- Issue
- Database
- Pages
- D434-D439
- Citations
- 93
- Access
- Closed
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Cite This
Andreas Schlicker,
M. Albrecht
(2007).
FunSimMat: a comprehensive functional similarity database.
Nucleic Acids Research
, 36
(Database)
, D434-D439.
https://doi.org/10.1093/nar/gkm806
Identifiers
- DOI
- 10.1093/nar/gkm806