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Tolerating some redundancy significantly speeds up clustering of large protein databases.
Li W, Jaroszewski L, Godzik A. Li W, et al. Bioinformatics. 2002 Jan;18(1):77-82. doi: 10.1093/bioinformatics/18.1.77. Bioinformatics. 2002. PMID: 11836214
Our previous program, CD-HI, clustered NR at 90% identity in approximately 1 h and at 75% identity in approximately 1 day on a 1 GHz Linux PC (Li et al., Bioinformatics, 17, 282, 2001); however even faster clustering speed is needed because the size of protein databases ar …
Our previous program, CD-HI, clustered NR at 90% identity in approximately 1 h and at 75% identity in approximately 1 day on a 1 GHz Linux P …
In search for more accurate alignments in the twilight zone.
Jaroszewski L, Li W, Godzik A. Jaroszewski L, et al. Protein Sci. 2002 Jul;11(7):1702-13. doi: 10.1110/ps.4820102. Protein Sci. 2002. PMID: 12070323 Free PMC article.
A segment alignment approach to protein comparison.
Ye Y, Jaroszewski L, Li W, Godzik A. Ye Y, et al. Bioinformatics. 2003 Apr 12;19(6):742-9. doi: 10.1093/bioinformatics/btg073. Bioinformatics. 2003. PMID: 12691986
FFAS03: a server for profile--profile sequence alignments.
Jaroszewski L, Rychlewski L, Li Z, Li W, Godzik A. Jaroszewski L, et al. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W284-8. doi: 10.1093/nar/gki418. Nucleic Acids Res. 2005. PMID: 15980471 Free PMC article.
Jaroszewski, W. Li and A. Godzik (2000), Protein Sci., 9, 232-241]. Profile-profile algorithms use information present in sequences of homologous proteins to amplify the patterns defining the family. ...
Jaroszewski, W. Li and A. Godzik (2000), Protein Sci., 9, 232-241]. Profile-profile algorithms use information present in sequ …
Identification of ribosomal RNA genes in metagenomic fragments.
Huang Y, Gilna P, Li W. Huang Y, et al. Bioinformatics. 2009 May 15;25(10):1338-40. doi: 10.1093/bioinformatics/btp161. Epub 2009 Apr 3. Bioinformatics. 2009. PMID: 19346323 Free PMC article.
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