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

Bioinformatics - Tập 22 Số 13 - Trang 1658-1659 - 2006
Weizhong Li1, Adam Godzik1
1Burnham Institute for Medical Research, La Jolla, CA 92037, USA

Tóm tắt

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:  [email protected]

Từ khóa


Tài liệu tham khảo

Apweiler, 2004, UniProt: the Universal Protein knowledgebase, Nucleic Acids Res., 32, D115, 10.1093/nar/gkh131

Bourne, 2004, The distribution and query systems of the RCSB Protein Data Bank, Nucleic Acids Res., 32, D223, 10.1093/nar/gkh096

Li, 2001, Clustering of highly homologous sequences to reduce the size of large protein databases, Bioinformatics, 17, 282, 10.1093/bioinformatics/17.3.282

Li, 2002, Sequence clustering strategies improve remote homology recognitions while reducing search times, Bioinformatics, 15, 643

Li, 2002, Tolerating some redundancy significantly speeds up clustering of large protein databases, Protein Eng., 18, 77

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Thông tin xuất bản

Bioinformatics

Tập 22 Số 13

1658-1659

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