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

• Published in: Bioinformatics Vol. 22; no. 13; pp. 1658 - 1659
• Main Authors: Li, Weizhong, Godzik, Adam
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01.07.2006; Oxford Publishing Limited (England)
• Subjects: Algorithms; Animals; Biological and medical sciences; Cluster Analysis; Computational Biology - methods; Databases, Nucleic Acid; Databases, Protein; DNA - chemistry; Expressed Sequence Tags; Fundamental and applied biological sciences. Psychology; General aspects; Humans; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Programming Languages; RNA - chemistry; Sequence Analysis, DNA - methods; Sequence Analysis, Protein - methods; Software; Computer program; Similarity; Nucleotide sequence; Database; Large scale; C++ language; Sequence; Bioinformatics; Scope note; Comparative study; Aminoacid sequence; Clusterin
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btl158

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: Contact:liwz@sdsc.edu