MotifCluster: an interactive online tool for clustering and visualizing sequences using shared motifs

Micah Hamady¹ , Jeremy Widmann² , Shelley D Copley³ and Rob Knight²

¹Department of Computer Science, University of Colorado, Boulder, CO 80309, USA

²Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA

³Department of Molecular, Cellular and Developmental Biology and Cooperative Institute for Research in Environmental Sciences (CIRES), University of Colorado, Boulder, CO 80309, USA

author email corresponding author email

Genome Biology 2008, 9:R128doi:10.1186/gb-2008-9-8-r128


Published:	15 August 2008

Subject areas: Bioinformatics, Evolution

Abstract

MotifCluster finds related motifs in a set of sequences, and clusters the sequences into families using the motifs they contain. MotifCluster, at http://bmf.colorado.edu/motifcluster webcite, lets users test whether proteins are related, cluster sequences by shared conserved motifs, and visualize motifs mapped onto trees, sequences and three-dimensional structures. We demonstrate MotifCluster's accuracy using gold-standard protein superfamilies; using recommended settings, families were assigned to the correct superfamilies with 0.17% false positive and no false negative assignments.