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Accelerated Profile HMM Searches.
Eddy SR. Eddy SR. PLoS Comput Biol. 2011 Oct;7(10):e1002195. doi: 10.1371/journal.pcbi.1002195. Epub 2011 Oct 20. PLoS Comput Biol. 2011. PMID: 22039361 Free PMC article.
Maximum discrimination hidden Markov models of sequence consensus.
Eddy SR, Mitchison G, Durbin R. Eddy SR, et al. J Comput Biol. 1995 Spring;2(1):9-23. doi: 10.1089/cmb.1995.2.9. J Comput Biol. 1995. PMID: 7497123
Pfam: multiple sequence alignments and HMM-profiles of protein domains.
Sonnhammer EL, Eddy SR, Birney E, Bateman A, Durbin R. Sonnhammer EL, et al. Among authors: eddy sr. 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. Among authors: eddy sr. 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.
Profile hidden Markov models.
Eddy SR. Eddy SR. Bioinformatics. 1998;14(9):755-63. doi: 10.1093/bioinformatics/14.9.755. Bioinformatics. 1998. PMID: 9918945 Review.
Query-dependent banding (QDB) for faster RNA similarity searches.
Nawrocki EP, Eddy SR. Nawrocki EP, et al. Among authors: eddy sr. 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.
A probabilistic model of local sequence alignment that simplifies statistical significance estimation.
Eddy SR. Eddy SR. PLoS Comput Biol. 2008 May 30;4(5):e1000069. doi: 10.1371/journal.pcbi.1000069. PLoS Comput Biol. 2008. PMID: 18516236 Free PMC article.
Probabilistic phylogenetic inference with insertions and deletions.
Rivas E, Eddy SR. Rivas E, et al. Among authors: eddy sr. PLoS Comput Biol. 2008 Sep 19;4(9):e1000172. doi: 10.1371/journal.pcbi.1000172. PLoS Comput Biol. 2008. PMID: 18787703 Free PMC article.
Local RNA structure alignment with incomplete sequence.
Kolbe DL, Eddy SR. Kolbe DL, et al. Among authors: eddy sr. Bioinformatics. 2009 May 15;25(10):1236-43. doi: 10.1093/bioinformatics/btp154. Epub 2009 Mar 20. Bioinformatics. 2009. PMID: 19304875 Free PMC article.
Infernal 1.0: inference of RNA alignments.
Nawrocki EP, Kolbe DL, Eddy SR. Nawrocki EP, et al. Among authors: eddy sr. Bioinformatics. 2009 May 15;25(10):1335-7. doi: 10.1093/bioinformatics/btp157. Epub 2009 Mar 23. Bioinformatics. 2009. PMID: 19307242 Free PMC article.
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