{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T00:37:45Z","timestamp":1783471065770,"version":"3.55.0"},"reference-count":23,"publisher":"Springer Science and Business Media LLC","issue":"S5","license":[{"start":{"date-parts":[[2007,5,1]],"date-time":"2007-05-01T00:00:00Z","timestamp":1177977600000},"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":[[2007,5]]},"DOI":"10.1186\/1471-2105-8-s5-s9","type":"journal-article","created":{"date-parts":[[2007,5,25]],"date-time":"2007-05-25T09:06:22Z","timestamp":1180083982000},"source":"Crossref","is-referenced-by-count":5,"title":["Automatic extraction of reliable regions from multiple sequence alignments"],"prefix":"10.1186","volume":"8","author":[{"given":"Timo","family":"Lassmann","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erik LL","family":"Sonnhammer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2007,5,24]]},"reference":[{"issue":"1\u20132","key":"1922_CR1","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1016\/S0378-1119(01)00461-9","volume":"270","author":"O Lecompte","year":"2001","unstructured":"Lecompte O, Thompson JD, Plewniak F, Thierry J, Poch O: Multiple alignment of complete sequences (MACS) in the post-genomic era. Gene 2001, 270(1\u20132):17\u201330. 10.1016\/S0378-1119(01)00461-9","journal-title":"Gene"},{"issue":"2","key":"1922_CR2","doi-asserted-by":"publisher","first-page":"330","DOI":"10.1101\/gr.2821705","volume":"15","author":"CB Do","year":"2005","unstructured":"Do CB, Mahabhashyam MS, Brudno M, Batzoglou S: ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res 2005, 15(2):330\u2013340. [\n                    http:\/\/www.genome.org\/cgi\/content\/abstract\/15\/2\/330\n                    \n                  ] 10.1101\/gr.2821705","journal-title":"Genome Res"},{"issue":"2","key":"1922_CR3","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1093\/nar\/gki198","volume":"33","author":"K Katoh","year":"2005","unstructured":"Katoh K, Kuma Ki, Toh H, Miyata T: MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucl Acids Res 2005, 33(2):511\u2013518. [\n                    http:\/\/nar.oxfordjournals.org\/cgi\/content\/abstract\/33\/2\/511\n                    \n                  ] 10.1093\/nar\/gki198","journal-title":"Nucl Acids Res"},{"key":"1922_CR4","doi-asserted-by":"publisher","first-page":"298","DOI":"10.1186\/1471-2105-6-298","volume":"6","author":"T Lassmann","year":"2005","unstructured":"Lassmann T, Sonnhammer E: Kalign \u2013 an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics 2005, 6: 298. [\n                    http:\/\/www.biomedcentral.com\/1471\u20132105\/6\/298\n                    \n                  ] 10.1186\/1471-2105-6-298","journal-title":"BMC Bioinformatics"},{"issue":"6","key":"1922_CR5","doi-asserted-by":"publisher","first-page":"1692","DOI":"10.1093\/nar\/gkl091","volume":"34","author":"IM Wallace","year":"2006","unstructured":"Wallace IM, O'Sullivan O, Higgins DG, Notredame C: M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucl Acids Res 2006, 34(6):1692\u20131699. [\n                    http:\/\/nar.oxfordjournals.org\/cgi\/content\/abstract\/34\/6\/1692\n                    \n                  ] 10.1093\/nar\/gkl091","journal-title":"Nucl Acids Res"},{"key":"1922_CR6","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1002\/prot.20527","volume":"61","author":"JD Thompson","year":"2005","unstructured":"Thompson JD, Koehl P, Ripp R, Poch O: BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark. Proteins 2005, 61: 127\u2013136. [JOURNAL ARTICLE] [JOURNAL ARTICLE] 10.1002\/prot.20527","journal-title":"Proteins"},{"issue":"7","key":"1922_CR7","doi-asserted-by":"publisher","first-page":"1267","DOI":"10.1093\/bioinformatics\/bth493","volume":"21","author":"I Van Walle","year":"2005","unstructured":"Van Walle I, Lasters I, Wyns L: SABmark-a benchmark for sequence alignment that covers the entire known fold space. Bioinformatics 2005, 21(7):1267\u20131268. [\n                    http:\/\/bioinformatics.oxfordjournals.org\/cgi\/content\/abstract\/21\/7\/1267\n                    \n                  ] 10.1093\/bioinformatics\/bth493","journal-title":"Bioinformatics"},{"issue":"4","key":"1922_CR8","doi-asserted-by":"publisher","first-page":"428","DOI":"10.1093\/oxfordjournals.molbev.a025779","volume":"14","author":"D Morrison","year":"1997","unstructured":"Morrison D, Ellis J: Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of apicomplexa. Mol Biol Evol 1997, 14(4):428\u2013441. [\n                    http:\/\/mbe.oxfordjournals.org\/cgi\/content\/abstract\/14\/4\/428\n                    \n                  ]","journal-title":"Mol Biol Evol"},{"issue":"2","key":"1922_CR9","doi-asserted-by":"publisher","first-page":"314","DOI":"10.1080\/10635150500541730","volume":"55","author":"TH Ogdenw","year":"2006","unstructured":"Ogdenw TH, Rosenberg MS: Multiple sequence alignment accuracy and phylogenetic inference. Syst Biol 2006, 55(2):314\u2013328. 10.1080\/10635150500541730","journal-title":"Syst Biol"},{"issue":"2","key":"1922_CR10","doi-asserted-by":"publisher","first-page":"170","DOI":"10.1093\/bioinformatics\/bth021","volume":"20","author":"K Sjolander","year":"2004","unstructured":"Sjolander K: Phylogenomic inference of protein molecular function: advances and challenges. Bioinformatics 2004, 20(2):170\u2013179. [\n                    http:\/\/bioinformatics.oxfordjournals.org\/cgi\/content\/abstract\/20\/2\/170\n                    \n                  ] 10.1093\/bioinformatics\/bth021","journal-title":"Bioinformatics"},{"issue":"22","key":"1922_CR11","doi-asserted-by":"publisher","first-page":"7120","DOI":"10.1093\/nar\/gki1020","volume":"33","author":"T Lassmann","year":"2005","unstructured":"Lassmann T, Sonnhammer ELL: Automatic assessment of alignment quality. Nucl Acids Res 2005, 33(22):7120\u20137128. [\n                    http:\/\/nar.oxfordjournals.org\/cgi\/content\/abstract\/33\/22\/7120\n                    \n                  ] 10.1093\/nar\/gki1020","journal-title":"Nucl Acids Res"},{"key":"1922_CR12","doi-asserted-by":"publisher","first-page":"318","DOI":"10.1186\/1471-2105-7-318","volume":"7","author":"J Thompson","year":"2006","unstructured":"Thompson J, Muller A, Waterhouse A, Procter J, Barton G, Plewniak F, Poch O: MACSIMS : Multiple Alignment of Complete Sequences Information Management System. BMC Bioinformatics 2006, 7: 318. [JOURNAL ARTICLE] [JOURNAL ARTICLE] 10.1186\/1471-2105-7-318","journal-title":"BMC Bioinformatics"},{"issue":"2","key":"1922_CR13","doi-asserted-by":"publisher","first-page":"W596","DOI":"10.1093\/nar\/gkl191","volume":"34","author":"T Lassmann","year":"2006","unstructured":"Lassmann T, Sonnhammer ELL: Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment. Nucl Acids Res 2006, 34(2):W596\u2013599. [\n                    http:\/\/nar.oxfordjournals.org\/cgi\/content\/abstract\/34\/suppl_2\/W596\n                    \n                  ] 10.1093\/nar\/gkl191","journal-title":"Nucl Acids Res"},{"key":"1922_CR14","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1093\/bioinformatics\/15.1.87","volume":"15","author":"J Thompson","year":"1999","unstructured":"Thompson J, Plewniak F, Poch O: BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics 1999, 15: 87\u201388. [\n                    http:\/\/bioinformatics.oxfordjournals.org\/cgi\/content\/abstract\/15\/1\/87\n                    \n                  ] 10.1093\/bioinformatics\/15.1.87","journal-title":"Bioinformatics"},{"issue":"5","key":"1922_CR15","doi-asserted-by":"publisher","first-page":"1792","DOI":"10.1093\/nar\/gkh340","volume":"32","author":"RC Edgar","year":"2004","unstructured":"Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl Acids Res 2004, 32(5):1792\u20131797. [\n                    http:\/\/nar.oxfordjournals.org\/cgi\/content\/abstract\/32\/5\/1792\n                    \n                  ] 10.1093\/nar\/gkh340","journal-title":"Nucl Acids Res"},{"issue":"2","key":"1922_CR16","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1093\/bioinformatics\/14.2.157","volume":"14","author":"J Stoye","year":"1998","unstructured":"Stoye J, Evers D, Meyer F: Rose: generating sequence families. Bioinformatics 1998, 14(2):157\u2013163. 10.1093\/bioinformatics\/14.2.157","journal-title":"Bioinformatics"},{"issue":"3","key":"1922_CR17","doi-asserted-by":"publisher","first-page":"452","DOI":"10.1093\/bioinformatics\/18.3.452","volume":"18","author":"C Lee","year":"2002","unstructured":"Lee C, Grasso C, Sharlow MF: Multiple sequence alignment using partial order graphs. Bioinformatics 2002, 18(3):452\u2013464. [\n                    http:\/\/bioinformatics.oxfordjournals.org\/cgi\/content\/abstract\/18\/3\/452\n                    \n                  ] 10.1093\/bioinformatics\/18.3.452","journal-title":"Bioinformatics"},{"issue":"10","key":"1922_CR18","doi-asserted-by":"publisher","first-page":"1546","DOI":"10.1093\/bioinformatics\/bth126","volume":"20","author":"C Grasso","year":"2004","unstructured":"Grasso C, Lee C: Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems. Bioinformatics 2004, 20(10):1546\u20131556. [\n                    http:\/\/bioinformatics.oxfordjournals.org\/cgi\/content\/abstract\/20\/10\/1546\n                    \n                  ] 10.1093\/bioinformatics\/bth126","journal-title":"Bioinformatics"},{"issue":"22","key":"1922_CR19","doi-asserted-by":"publisher","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","volume":"22","author":"JD Thompson","year":"1994","unstructured":"Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl Acids Res 1994, 22(22):4673\u20134680. [\n                    http:\/\/nar.oxfordjournals.org\/cgi\/content\/abstract\/22\/22\/4673\n                    \n                  ] 10.1093\/nar\/22.22.4673","journal-title":"Nucl Acids Res"},{"issue":"3","key":"1922_CR20","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1093\/bioinformatics\/14.3.290","volume":"14","author":"B Morgenstern","year":"1998","unstructured":"Morgenstern B, Frech K, Dress A, Werner T: DIALIGN: finding local similarities by multiple sequence alignment. Bioinformatics 1998, 14(3):290\u2013294. [\n                    http:\/\/bioinformatics.oxfordjournals.org\/cgi\/content\/abstract\/14\/3\/290\n                    \n                  ] 10.1093\/bioinformatics\/14.3.290","journal-title":"Bioinformatics"},{"issue":"3","key":"1922_CR21","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1093\/bioinformatics\/15.3.211","volume":"15","author":"B Morgenstern","year":"1999","unstructured":"Morgenstern B: DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 1999, 15(3):211\u2013218. [\n                    http:\/\/bioinformatics.oxfordjournals.org\/cgi\/content\/abstract\/15\/3\/211\n                    \n                  ] 10.1093\/bioinformatics\/15.3.211","journal-title":"Bioinformatics"},{"issue":"14","key":"1922_CR22","doi-asserted-by":"publisher","first-page":"3059","DOI":"10.1093\/nar\/gkf436","volume":"30","author":"K Katoh","year":"2002","unstructured":"Katoh K, Misawa K, Kuma Ki, Miyata T: MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucl Acids Res 2002, 30(14):3059\u20133066. [\n                    http:\/\/nar.oxfordjournals.org\/cgi\/content\/abstract\/30\/14\/3059\n                    \n                  ] 10.1093\/nar\/gkf436","journal-title":"Nucl Acids Res"},{"key":"1922_CR23","doi-asserted-by":"publisher","first-page":"205","DOI":"10.1006\/jmbi.2000.4042","volume":"302","author":"C Notredame","year":"2000","unstructured":"Notredame C, Higgins DG, Heringa J: T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000, 302: 205\u2013217. 10.1006\/jmbi.2000.4042","journal-title":"J Mol Biol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-8-S5-S9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-8-S5-S9\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-8-S5-S9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,23]],"date-time":"2019-01-23T08:52:54Z","timestamp":1548233574000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-8-S5-S9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,5]]},"references-count":23,"journal-issue":{"issue":"S5","published-print":{"date-parts":[[2007,5]]}},"alternative-id":["1922"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-8-s5-s9","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,5]]},"article-number":"S9"}}