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Bioinformatics Advance Access originally published online on May 26, 2006
Bioinformatics 2006 22(13):1658-1659; doi:10.1093/bioinformatics/btl158
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Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

Weizhong Li * and Adam Godzik

Burnham Institute for Medical Research La Jolla, CA 92037, USA

*To whom correspondence should be addressed.

Motivation: In 2001 and 2002, we published two papers (Bioinformatics, 17, 282–283, Bioinformatics, 18, 77–82) describing an ultrafast protein sequence clustering program called cd-hit. This program can efficiently cluster a huge protein database with millions of sequences. However, the applications of the underlying algorithm are not limited to only protein sequences clustering, here we present several new programs using the same algorithm including cd-hit-2d, cd-hit-est and cd-hit-est-2d. Cd-hit-2d compares two protein datasets and reports similar matches between them; cd-hit-est clusters a DNA/RNA sequence database and cd-hit-est-2d compares two nucleotide datasets. All these programs can handle huge datasets with millions of sequences and can be hundreds of times faster than methods based on the popular sequence comparison and database search tools, such as BLAST.

Availability: http://cd-hit.org

Contact: liwz{at}sdsc.edu

Received on March 23, 2006; revised on April 20, 2006; accepted on April 20, 2006

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