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Bioinformatics Advance Access published online on May 26, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl158
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© 2006 The Author(s)
Received March 23, 2006
Revised April 20, 2006
Accepted April 20, 2006

Applications note

cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

Weizhong Li 1 * and Adam Godzik 1

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

* To whom correspondence should be addressed.
Weizhong Li, E-mail: liwz{at}sdsc.edu


  Abstract

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 data sets and reports similar matches between them; cd-hit-est clusters a DNA/RNA sequence database; and cd-hit-est-2d compares two nucleotide data sets. All these programs can handle huge data sets 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.

Associate Editor: Golan Yona
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