SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale

Background: An important problem in genomics is the automatic inference of groups of homologous proteins from pairwise sequence similarities. Several approaches have been proposed for this task which are "local" in the sense that they assign a protein to a cluster based only on the distances between that protein and the other proteins in the set. It was shown recently that global methods such as spectral clustering have better performance on a wide variety of datasets. However, currently available implementations of spectral clustering methods mostly consist of a few loosely coupled Matlab scripts that assume a fair amount of familiarity with Matlab programming and hence they are inaccessible for large parts of the research community. Results: SCPS (Spectral Clustering of Protein Sequences) is an efficient and user-friendly implementation of a spectral method for inferring protein families. The method uses only pairwise sequence similarities, and is therefore practical when ...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Tamás Nepusz, Rajkumar Sasidharan, Alberto Paccanaro
• Keywords: BMCBI 2010, Protein, Sequence Similarities, Spectral Clustering