Abstract
MotifCluster finds related motifs in a set of sequences and clusters the sequences into families using the motifs they contain.
Highlights
Detection of evolutionary relationships between very distantly related protein families is important for efforts to assign functions to newly identified proteins, as well as to understand the evolutionary mechanisms by which new functions have emerged
Identification of short, highly conserved sequences, known as motifs, in proteins provides important insights into the regions of proteins that have been conserved within a superfamily or suprafamily, as well as those that have diverged in specific families. Consideration of these motifs in conjunction with mechanistic and structural information can provide a picture of the sequence changes that led to acquisition of new catalytic capabilities
A background probability model for chance matches based on amino acid occurrences is determined from the input set of Genome Biology 2008, 9:R128 http://genomebiology.com/2008/9/8/R128
Summary
MotifCluster: an interactive online tool for clustering and visualizing sequences using shared motifs. Addresses: *Department of Computer Science, University of Colorado, Boulder, CO 80309, USA. The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2008/9/8/R128
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