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 accessAbstract
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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Cites
Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach
Manichanh, C., Rigottier-Gois, L., Bonnaud, E., Gloux, K., Pelletier, E., Frangeul, L., Nalin, R., Jarrin, C., Chardon, P., Marteau, P., et al. (2006) · Gut · doi:10.1136/gut.2005.073817 · Cited by 2,277
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Research works printed but not linked: 5
- Apweiler, 2004, UniProt: the Universal Protein knowledgebase, Nucleic Acids Res., 32, D115, 10.1093/nar/gkh131 · DOI
- Bourne, 2004, The distribution and query systems of the RCSB Protein Data Bank, Nucleic Acids Res., 32, D223, 10.1093/nar/gkh096 · DOI
- 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
- 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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Hemm, L., Rabsch, D., Ropp, H. R., Reimann, V., Gerth, P., Bartel, J., Brenes-Álvarez, M., Maaß, S., Becher, D., Hess, W. R., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-64086-7 · Cited by 5
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Minami, A., Nishi, K., Yamada, R., Jinnai, G., Shima, H., Oishi, S., Akagawa, H., Aono, T., Hidaka, M., Masaki, H., et al. (2025) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2025.108554 · Cited by 4
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“DPAM domains were clustered by sequence using CD-HIT [36–38] at 40%, 70%, and 99% thresholds using a bandwidth of 20, min_length of 10, and tolerance of 2.”
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“The redundancy across the identified NUDIX sequences was first reduced with cd-hit (70% sequence identity, 90% coverage, 5 letters word length) [10].”
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Caspase-1 activates gasdermin A in non-mammals
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Protein tandem repeats that produce frameshifts can generate new structural states and functions
Osmanli, Z., Aldrian, G., Leclercq, J., Falgarone, T., Gómez Bergna, S. M., Prada Gori, D. N., Oleinikov, A. V., Shahmuradov, I., & Kajava, A. V. (2026) · The FEBS Journal · doi:10.1111/febs.70273
AFFIPred : AlphaFold2 structure‐based Functional Impact Prediction of missense variations
Pir, M. S., & Timucin, E. (2025) · Protein Science · doi:10.1002/pro.70030
Tran, N. D., Subramani, K., & Su, C. T.-T. (2025) · mAbs · doi:10.1080/19420862.2025.2531227
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
- OpenAlex
- W2156125289
- Cited by
- 11,410
- References
- 3
- FWCI
- 30.70
- Type
- journal article
- Language
- en
- Open access
- hybrid
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