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Cited by 11,410

The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.

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

Open access
Li, Weizhong, Godzik, Adam·2006·Bioinformatics
DOI 10.1093/bioinformatics/btl158
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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 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

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Research works printed but not linked: 5

  1. Apweiler, 2004, UniProt: the Universal Protein knowledgebase, Nucleic Acids Res., 32, D115, 10.1093/nar/gkh131 · DOI
  2. Bourne, 2004, The distribution and query systems of the RCSB Protein Data Bank, Nucleic Acids Res., 32, D223, 10.1093/nar/gkh096 · DOI
  3. Li, 2001, Clustering of highly homologous sequences to reduce the size of large protein databases, Bioinformatics, 17, 282, 10.1093/bioinformatics/17.3.282 · DOI · Paper page
  4. Li, 2002, Sequence clustering strategies improve remote homology recognitions while reducing search times, Bioinformatics, 15, 643
  5. Li, 2002, Tolerating some redundancy significantly speeds up clustering of large protein databases, Protein Eng., 18, 77

Cited by

Metadata

Authors
Li, W., & Godzik, A.
Venue
Bioinformatics
Publisher
Oxford University Press (OUP)
Published
2006-05-26
Volume
22
Issue
13
Pages
1658-1659
ISSN
  • 1367-4803 (ISSN-L)
  • 1367-4811
DOI
10.1093/bioinformatics/btl158
OpenAlex
W2156125289
Cited by
11,410
References
3
FWCI
30.70
Type
journal article
Language
en
Open access
hybrid

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