{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,19]],"date-time":"2025-09-19T08:39:36Z","timestamp":1758271176048},"reference-count":26,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2008,1,30]],"date-time":"2008-01-30T00:00:00Z","timestamp":1201651200000},"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":[[2008,12]]},"DOI":"10.1186\/1471-2105-9-72","type":"journal-article","created":{"date-parts":[[2008,1,30]],"date-time":"2008-01-30T19:14:16Z","timestamp":1201720456000},"source":"Crossref","is-referenced-by-count":15,"title":["Subfamily specific conservation profiles for proteins based on n-gram patterns"],"prefix":"10.1186","volume":"9","author":[{"given":"John K","family":"Vries","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiong","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2008,1,30]]},"reference":[{"key":"2057_CR1","first-page":"2132","volume":"35","author":"MO Dayhoff","year":"1976","unstructured":"Dayhoff MO: The origin and evolution of protein superfamilies. Fed Proc 1976, 35: 2132\u20132138.","journal-title":"Fed Proc"},{"key":"2057_CR2","doi-asserted-by":"publisher","first-page":"10915","DOI":"10.1073\/pnas.89.22.10915","volume":"89","author":"S Henikoff","year":"1992","unstructured":"Henikoff S, Henikoff JG: Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A 1992, 89: 10915\u201310919. 10.1073\/pnas.89.22.10915","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2057_CR3","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1006\/jmbi.2001.5034","volume":"313","author":"WS Valdar","year":"2001","unstructured":"Valdar WS, Thornton JM: Conservation helps to identify biologically relevant crystal contacts. J Mol Biol 2001, 313: 399\u2013416. 10.1006\/jmbi.2001.5034","journal-title":"J Mol Biol"},{"key":"2057_CR4","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1002\/1097-0134(20010101)42:1<108::AID-PROT110>3.0.CO;2-O","volume":"42","author":"WS Valdar","year":"2001","unstructured":"Valdar WS, Thornton JM: Protein-protein interfaces: analysis of amino acid conservation in homodimers. Proteins 2001, 42: 108\u2013124. 10.1002\/1097-0134(20010101)42:1<108::AID-PROT110>3.0.CO;2-O","journal-title":"Proteins"},{"key":"2057_CR5","doi-asserted-by":"publisher","first-page":"555","DOI":"10.1016\/0022-2836(91)90193-A","volume":"219","author":"SF Altschul","year":"1991","unstructured":"Altschul SF: Amino acid substitution matrices from an information theoretic perspective. J Mol Biol 1991, 219: 555\u2013565. 10.1016\/0022-2836(91)90193-A","journal-title":"J Mol Biol"},{"key":"2057_CR6","doi-asserted-by":"publisher","first-page":"628","DOI":"10.1128\/EC.5.4.628-637.2006","volume":"5","author":"JE Coronado","year":"2006","unstructured":"Coronado JE, Attie O, Epstein SL, Qiu WG, Lipke PN: Composition-modified matrices improve identification of homologs of saccharomyces cerevisiae low-complexity glycoproteins. Eukaryot Cell 2006, 5: 628\u2013637. 10.1128\/EC.5.4.628-637.2006","journal-title":"Eukaryot Cell"},{"key":"2057_CR7","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1002\/prot.340170108","volume":"17","author":"S Henikoff","year":"1993","unstructured":"Henikoff S, Henikoff JG: Performance evaluation of amino acid substitution matrices. Proteins 1993, 17: 49\u201361. 10.1002\/prot.340170108","journal-title":"Proteins"},{"key":"2057_CR8","doi-asserted-by":"publisher","first-page":"716","DOI":"10.1006\/jmbi.1993.1548","volume":"233","author":"MS Johnson","year":"1993","unstructured":"Johnson MS, Overington JP: A structural basis for sequence comparisons. An evaluation of scoring methodologies. J Mol Biol 1993, 233: 716\u2013738. 10.1006\/jmbi.1993.1548","journal-title":"J Mol Biol"},{"key":"2057_CR9","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1186\/1471-2105-4-47","volume":"4","author":"GP Raghava","year":"2003","unstructured":"Raghava GP, Searle SM, Audley PC, Barber JD, Barton GJ: OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy. BMC Bioinformatics 2003, 4: 47. 10.1186\/1471-2105-4-47","journal-title":"BMC Bioinformatics"},{"key":"2057_CR10","doi-asserted-by":"publisher","first-page":"554","DOI":"10.1016\/S0076-6879(96)66035-2","volume":"266","author":"JC Wootton","year":"1996","unstructured":"Wootton JC, Federhen S: Analysis of compositionally biased regions in sequence databases. Methods Enzymol 1996, 266: 554\u2013571.","journal-title":"Methods Enzymol"},{"key":"2057_CR11","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/bioinformatics\/14.9.772","volume":"14","author":"R Karchin","year":"1998","unstructured":"Karchin R, Hughey R: Weighting hidden Markov models for maximum discrimination. Bioinformatics 1998, 14: 772\u2013782. 10.1093\/bioinformatics\/14.9.772","journal-title":"Bioinformatics"},{"key":"2057_CR12","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: 3389\u20133402. 10.1093\/nar\/25.17.3389","journal-title":"Nucleic Acids Res"},{"key":"2057_CR13","doi-asserted-by":"publisher","first-page":"137","DOI":"10.2165\/00822942-200403020-00008","volume":"3","author":"JK Vries","year":"2004","unstructured":"Vries JK, Munshi R, Tobi D, Klein-Seetharaman J, Benos PV, Bahar I: A sequence alignment-independent method for protein classification. Appl Bioinformatics 2004, 3: 137\u2013148. 10.2165\/00822942-200403020-00008","journal-title":"Appl Bioinformatics"},{"key":"2057_CR14","doi-asserted-by":"publisher","first-page":"830","DOI":"10.1002\/prot.21480","volume":"68","author":"JK Vries","year":"2007","unstructured":"Vries JK, Liu X, Bahar I: The relationship between n-gram patterns and protein secondary structure. Proteins 2007, 68: 830\u2013838. 10.1002\/prot.21480","journal-title":"Proteins"},{"key":"2057_CR15","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1002\/prot.10032","volume":"46","author":"F Fogolari","year":"2002","unstructured":"Fogolari F, Tessari S, Molinari H: Singular value decomposition analysis of protein sequence alignment score data. Proteins 2002, 46: 161\u2013170. 10.1002\/prot.10032","journal-title":"Proteins"},{"key":"2057_CR16","unstructured":"The Universal Protein Resource (UniProt)[\n                    http:\/\/www.pir.uniprot.org\/\n                    \n                  ]"},{"key":"2057_CR17","doi-asserted-by":"publisher","first-page":"D247","DOI":"10.1093\/nar\/gkj149","volume":"34","author":"RD Finn","year":"2006","unstructured":"Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A: Pfam: clans, web tools and services. Nucleic Acids Res 2006, 34: D247-D251. 10.1093\/nar\/gkj149","journal-title":"Nucleic Acids Res"},{"key":"2057_CR18","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1002\/bimj.200410102","volume":"47","author":"H Joe","year":"2005","unstructured":"Joe H, Zhu R: Generalized Poisson distribution: the property of mixture of Poisson and comparison with negative binomial distribution. Biom J 2005, 47: 219\u2013229. 10.1002\/bimj.200410102","journal-title":"Biom J"},{"key":"2057_CR19","unstructured":"Java 1.5.0[\n                    http:\/\/java.sun.com\/j2se\/1.5.0\n                    \n                  ]"},{"key":"2057_CR20","volume-title":"Applied Nonparametric Regression","author":"H W.","year":"1990","unstructured":"W. H: Applied Nonparametric Regression. Cambridge, Cambridge University Press; 1990."},{"key":"2057_CR21","doi-asserted-by":"publisher","first-page":"518","DOI":"10.1002\/prot.20221","volume":"57","author":"Y Hou","year":"2004","unstructured":"Hou Y, Hsu W, Lee ML, Bystroff C: Remote homolog detection using local sequence-structure correlations. Proteins 2004, 57: 518\u2013530. 10.1002\/prot.20221","journal-title":"Proteins"},{"key":"2057_CR22","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1093\/bioinformatics\/bti801","volume":"22","author":"QW Dong","year":"2006","unstructured":"Dong QW, Wang XL, Lin L: Application of latent semantic analysis to protein remote homology detection. Bioinformatics 2006, 22: 285\u2013290. 10.1093\/bioinformatics\/bti801","journal-title":"Bioinformatics"},{"key":"2057_CR23","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1016\/S1359-0278(97)00024-2","volume":"2","author":"I Bahar","year":"1997","unstructured":"Bahar I, Atilgan AR, Erman B: Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des 1997, 2: 173\u2013181. 10.1016\/S1359-0278(97)00024-2","journal-title":"Fold Des"},{"key":"2057_CR24","volume-title":"Proc Natl Inst Sci India","author":"PC Mahalanobis","year":"1936","unstructured":"Mahalanobis PC: On the generalised distance in statistics. Proc Natl Inst Sci India 1936."},{"key":"2057_CR25","unstructured":"The Pfam ftp site2008. [\n                    ftp:\/\/ftp.sanger.ac.uk\/pub\/databases\/Pfam\/current_release\n                    \n                  ]"},{"key":"2057_CR26","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1002\/prot.10146","volume":"48","author":"WS Valdar","year":"2002","unstructured":"Valdar WS: Scoring residue conservation. Proteins 2002, 48: 227\u2013241. 10.1002\/prot.10146","journal-title":"Proteins"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-72.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-9-72\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-72.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T08:55:30Z","timestamp":1548147330000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-9-72"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,1,30]]},"references-count":26,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2008,12]]}},"alternative-id":["2057"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-9-72","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,1,30]]},"article-number":"72"}}