{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T18:30:02Z","timestamp":1775759402089,"version":"3.50.1"},"reference-count":16,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2010,8,18]],"date-time":"2010-08-18T00:00:00Z","timestamp":1282089600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2010,12]]},"DOI":"10.1186\/1471-2105-11-431","type":"journal-article","created":{"date-parts":[[2010,8,19]],"date-time":"2010-08-19T06:13:47Z","timestamp":1282198427000},"source":"Crossref","is-referenced-by-count":1228,"title":["Hidden Markov model speed heuristic and iterative HMM search procedure"],"prefix":"10.1186","volume":"11","author":[{"given":"L Steven","family":"Johnson","sequence":"first","affiliation":[]},{"given":"Sean R","family":"Eddy","sequence":"additional","affiliation":[]},{"given":"Elon","family":"Portugaly","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2010,8,18]]},"reference":[{"key":"3888_CR1","unstructured":"HMMER: biosequence analysis using profile hidden Markov models[\n                    http:\/\/hmmer.org\/\n                    \n                  ]"},{"key":"3888_CR2","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"3","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 3: 403\u2013410.","journal-title":"J Mol Biol"},{"issue":"17","key":"3888_CR3","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"SF Altschul","year":"1997","unstructured":"Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389\u20133402. 10.1093\/nar\/25.17.3389","journal-title":"Nucleic Acids Res"},{"issue":"10","key":"3888_CR4","doi-asserted-by":"publisher","first-page":"846","DOI":"10.1093\/bioinformatics\/14.10.846","volume":"14","author":"K Karplus","year":"1998","unstructured":"Karplus K, Barrett C, Hughey R: Hidden Markov models for detecting remote protein homologies. Bioinformatics 1998, 14(10):846\u2013856. 10.1093\/bioinformatics\/14.10.846","journal-title":"Bioinformatics"},{"key":"3888_CR5","doi-asserted-by":"publisher","first-page":"410","DOI":"10.1186\/1471-2105-7-410","volume":"7","author":"ED Scheeff","year":"2006","unstructured":"Scheeff ED, Bourne PE: Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction. BMC Bioinformatics 2006, 7: 410. 10.1186\/1471-2105-7-410","journal-title":"BMC Bioinformatics"},{"key":"3888_CR6","doi-asserted-by":"publisher","first-page":"2994","DOI":"10.1093\/nar\/29.14.2994","volume":"29","author":"AA Schaffer","year":"2001","unstructured":"Schaffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf YI, Koonin EV, Altschul SF: Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res 2001, 29: 2994\u20133005. 10.1093\/nar\/29.14.2994","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"3888_CR7","doi-asserted-by":"publisher","first-page":"423","DOI":"10.1093\/bioinformatics\/14.5.423","volume":"14","author":"L Holm","year":"1998","unstructured":"Holm L, Sander C: Removing near-neighbour redundancy from large protein sequence collections. Bioinformatics 1998, 14(5):423\u2013429. 10.1093\/bioinformatics\/14.5.423","journal-title":"Bioinformatics"},{"issue":"11","key":"3888_CR8","doi-asserted-by":"publisher","first-page":"6073","DOI":"10.1073\/pnas.95.11.6073","volume":"95","author":"SE Brenner","year":"1998","unstructured":"Brenner SE, Chothia C, Hubbard TJ: Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc Natl Acad Sci USA 1998, 95(11):6073\u20136078. 10.1073\/pnas.95.11.6073","journal-title":"Proc Natl Acad Sci USA"},{"issue":"1","key":"3888_CR9","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1093\/nar\/28.1.257","volume":"28","author":"L Lo Conte","year":"2000","unstructured":"Lo Conte L, Ailey B, Hubbard TJ, Brenner SE, Murzin AG, Chothia C: SCOP: a structural classification of proteins database. Nucleic Acids Res 2000, 28(1):257\u2013259. 10.1093\/nar\/28.1.257","journal-title":"Nucleic Acids Res"},{"key":"3888_CR10","doi-asserted-by":"publisher","first-page":"D281","DOI":"10.1093\/nar\/gkm960","volume":"36","author":"RD Finn","year":"2008","unstructured":"Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A: The Pfam protein families database. Nucleic Acids Res 2008, 36: D281\u20138. 10.1093\/nar\/gkm960","journal-title":"Nucleic Acids Res"},{"key":"3888_CR11","doi-asserted-by":"publisher","first-page":"254","DOI":"10.1093\/nar\/28.1.254","volume":"28","author":"SE Brenner","year":"2000","unstructured":"Brenner SE, Koehl P, Levitt M: The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res 2000, 28: 254\u2013256. 10.1093\/nar\/28.1.254","journal-title":"Nucleic Acids Res"},{"key":"3888_CR12","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1093\/nar\/30.1.260","volume":"30","author":"JM Chandonia","year":"2002","unstructured":"Chandonia JM, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE: ASTRAL compendium enhancements. Nucleic Acids Res 2002, 30: 260\u2013263. 10.1093\/nar\/30.1.260","journal-title":"Nucleic Acids Res"},{"issue":"19","key":"3888_CR13","doi-asserted-by":"publisher","first-page":"4321","DOI":"10.1093\/nar\/gkf544","volume":"30","author":"M Madera","year":"2002","unstructured":"Madera M, Gough J: A comparison of profile hidden Markov model procedures for remote homology detection. Nucleic Acids Res 2002, 30(19):4321\u20134328. 10.1093\/nar\/gkf544","journal-title":"Nucleic Acids Res"},{"key":"3888_CR14","doi-asserted-by":"publisher","first-page":"1145","DOI":"10.1002\/pro.5560040613","volume":"4","author":"WR Pearson","year":"1995","unstructured":"Pearson WR: Comparison of methods for searching protein sequence databases. Protein Sci 1995, 4: 1145\u20131160. 10.1002\/pro.5560040613","journal-title":"Protein Sci"},{"key":"3888_CR15","doi-asserted-by":"publisher","first-page":"3824","DOI":"10.1093\/bioinformatics\/bti627","volume":"21","author":"GA Price","year":"2005","unstructured":"Price GA, Crooks GE, Green RE, Brenner SE: Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap. Bioinformatics 2005, 21: 3824\u20133831. 10.1093\/bioinformatics\/bti627","journal-title":"Bioinformatics"},{"issue":"3","key":"3888_CR16","doi-asserted-by":"publisher","first-page":"479","DOI":"10.1089\/cmb.1998.5.479","volume":"5","author":"WN Grundy","year":"1998","unstructured":"Grundy WN: Homology detection via family pairwise search. J Comput Biol 1998, 5(3):479\u2013491. 10.1089\/cmb.1998.5.479","journal-title":"J Comput Biol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-11-431.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-11-431\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-11-431.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T13:44:52Z","timestamp":1548164692000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-11-431"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,8,18]]},"references-count":16,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2010,12]]}},"alternative-id":["3888"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-11-431","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,8,18]]},"article-number":"431"}}