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HMMER web server: interactive sequence similarity searching.
Finn RD, Clements J, Eddy SR. Finn RD, et al. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W29-37. doi: 10.1093/nar/gkr367. Epub 2011 May 18. Nucleic Acids Res. 2011. PMID: 21593126 Free PMC article.
Pfam: multiple sequence alignments and HMM-profiles of protein domains.
Sonnhammer EL, Eddy SR, Birney E, Bateman A, Durbin R. Sonnhammer EL, et al. Nucleic Acids Res. 1998 Jan 1;26(1):320-2. doi: 10.1093/nar/26.1.320. Nucleic Acids Res. 1998. PMID: 9399864 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.
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.
The Pfam protein families database.
Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL. Bateman A, et al. Nucleic Acids Res. 2002 Jan 1;30(1):276-80. doi: 10.1093/nar/30.1.276. Nucleic Acids Res. 2002. PMID: 11752314 Free PMC article.
Rfam: an RNA family database.
Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR. Griffiths-Jones S, et al. Nucleic Acids Res. 2003 Jan 1;31(1):439-41. doi: 10.1093/nar/gkg006. Nucleic Acids Res. 2003. PMID: 12520045 Free PMC article.
The Pfam protein families database.
Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR. Bateman A, et al. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D138-41. doi: 10.1093/nar/gkh121. Nucleic Acids Res. 2004. PMID: 14681378 Free PMC article.
Rfam: annotating non-coding RNAs in complete genomes.
Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A. Griffiths-Jones S, et al. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D121-4. doi: 10.1093/nar/gki081. Nucleic Acids Res. 2005. PMID: 15608160 Free PMC article.
Pfam: clans, web tools and services.
Finn RD, Mistry J, Schuster-Böckler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A. Finn RD, et al. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D247-51. doi: 10.1093/nar/gkj149. Nucleic Acids Res. 2006. PMID: 16381856 Free PMC article.
Query-dependent banding (QDB) for faster RNA similarity searches.
Nawrocki EP, Eddy SR. Nawrocki EP, et al. PLoS Comput Biol. 2007 Mar 30;3(3):e56. doi: 10.1371/journal.pcbi.0030056. Epub 2007 Feb 7. PLoS Comput Biol. 2007. PMID: 17397253 Free PMC article.
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