Cd hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
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.
Bioinform.