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A workbench for large-scale sequence homology analysis.
Sonnhammer EL, Durbin R. Sonnhammer EL, et al. Comput Appl Biosci. 1994 Jun;10(3):301-7. doi: 10.1093/bioinformatics/10.3.301. Comput Appl Biosci. 1994. PMID: 7922687
The Pfam protein families database.
Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD. Punta M, et al. Nucleic Acids Res. 2012 Jan;40(Database issue):D290-301. doi: 10.1093/nar/gkr1065. Epub 2011 Nov 29. Nucleic Acids Res. 2012. PMID: 22127870 Free PMC article.
The Pfam protein families database.
Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A. Finn RD, et al. Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22. doi: 10.1093/nar/gkp985. Epub 2009 Nov 17. Nucleic Acids Res. 2010. PMID: 19920124 Free PMC article.
An expert system for processing sequence homology data.
Sonnhammer EL, Durbin R. Sonnhammer EL, et al. Proc Int Conf Intell Syst Mol Biol. 1994;2:363-8. Proc Int Conf Intell Syst Mol Biol. 1994. PMID: 7584413
Pfam: a comprehensive database of protein domain families based on seed alignments.
Sonnhammer EL, Eddy SR, Durbin R. Sonnhammer EL, et al. Proteins. 1997 Jul;28(3):405-20. doi: 10.1002/(sici)1097-0134(199707)28:3<405::aid-prot10>3.0.co;2-l. Proteins. 1997. PMID: 9223186
Volume changes in protein evolution.
Gerstein M, Sonnhammer EL, Chothia C. Gerstein M, et al. J Mol Biol. 1994 Mar 4;236(4):1067-78. doi: 10.1016/0022-2836(94)90012-4. J Mol Biol. 1994. PMID: 8120887
The Pfam protein families database.
Bateman A, Birney E, Durbin R, Eddy SR, Howe KL, Sonnhammer EL. Bateman A, et al. Nucleic Acids Res. 2000 Jan 1;28(1):263-6. doi: 10.1093/nar/28.1.263. Nucleic Acids Res. 2000. PMID: 10592242 Free PMC article.
Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins.
Bateman A, Birney E, Durbin R, Eddy SR, Finn RD, Sonnhammer EL. Bateman A, et al. Nucleic Acids Res. 1999 Jan 1;27(1):260-2. doi: 10.1093/nar/27.1.260. Nucleic Acids Res. 1999. PMID: 9847196 Free PMC article.
Analysis of protein domain families in Caenorhabditis elegans.
Sonnhammer EL, Durbin R. Sonnhammer EL, et al. Genomics. 1997 Dec 1;46(2):200-16. doi: 10.1006/geno.1997.4989. Genomics. 1997. PMID: 9417907
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