The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Clustering of highly homologous sequences to reduce the size of large protein databases
Abstract
Summary: We present a fast and flexible program for clustering large protein databases at different sequence identity levels. It takes less than 2 h for the all-against-all sequence comparison and clustering of the non-redundant protein database of over 560000 sequences on a high-end PC. The output database, including only the representative sequences, can be used for more efficient and sensitive database searches. Availability: The program is available from http://bioinformatics.burnham-inst.org/cd-hi Contact: liwz@sdsc.edu or adam@burnham-inst.org * To whom correspondence should be addressed.
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Citations
Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
Cited by
Cd-hit: Accelerated for clustering the next-generation sequencing data
Fu, L., Niu, B., Zhu, Z., Wu, S., & Li, W. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts565 · Cited by 11,175
Self-citationMAFFT online service: multiple sequence alignment, interactive sequence choice and visualization
Katoh, K., Rozewicki, J., & Yamada, K. D. (2019) · Briefings in Bioinformatics · doi:10.1093/bib/bbx108 · Cited by 8,909
UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches
Suzek, B. E., Wang, Y., Huang, H., McGarvey, P. B., Wu, C. H., & the UniProt Consortium (2015) · Bioinformatics · doi:10.1093/bioinformatics/btu739 · Cited by 1,928
One thousand plant transcriptomes and the phylogenomics of green plants
Initiative, O. T. P. T. (2019) · Nature · doi:10.1038/s41586-019-1693-2 · Cited by 1,734
UniRef: comprehensive and non-redundant UniProt reference clusters
Suzek, B. E., Huang, H., McGarvey, P., Mazumder, R., & Wu, C. H. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm098 · Cited by 1,613
Metadata
- Authors
- Li, W., Jaroszewski, L., & Godzik, A.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2001-03-01
- Volume
- 17
- Issue
- 3
- Pages
- 282-283
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2108211735
- Cited by
- 1,034
- References
- 1
- FWCI
- 5.75
- Type
- journal article
- Language
- en
- Open access
- closed
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- Li, W., Jaroszewski, L., & Godzik, A. (2001). Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics. https://doi.org/10.1093/bioinformatics/17.3.282
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