{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,7]],"date-time":"2026-02-07T16:45:35Z","timestamp":1770482735927,"version":"3.49.0"},"reference-count":46,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2014,12]]},"DOI":"10.1186\/1471-2105-15-265","type":"journal-article","created":{"date-parts":[[2014,8,7]],"date-time":"2014-08-07T01:03:15Z","timestamp":1407373395000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["ReformAlign: improved multiple sequence alignments using a profile-based meta-alignment approach"],"prefix":"10.1186","volume":"15","author":[{"given":"Dimitrios P","family":"Lyras","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dirk","family":"Metzler","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2014,8,7]]},"reference":[{"key":"6534_CR1","doi-asserted-by":"publisher","first-page":"e123","DOI":"10.1371\/journal.pcbi.0030123","volume":"3","author":"C Notredame","year":"2007","unstructured":"Notredame C: Recent evolutions of multiple sequence alignment algorithms. PLoS Comput Biol. 2007, 3: e123.","journal-title":"PLoS Comput Biol"},{"key":"6534_CR2","doi-asserted-by":"publisher","first-page":"368","DOI":"10.1016\/j.sbi.2006.04.004","volume":"16","author":"RC Edgar","year":"2006","unstructured":"Edgar RC, Batzoglou S: Multiple sequence alignment. Curr Opin Struct Biol. 2006, 16: 368-373.","journal-title":"Curr Opin Struct Biol"},{"key":"6534_CR3","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1517\/14622416.3.1.131","volume":"3","author":"C Notredame","year":"2002","unstructured":"Notredame C: Recent progress in multiple sequence alignment: a survey. Pharmacogenomics. 2002, 3: 131-144.","journal-title":"Pharmacogenomics"},{"key":"6534_CR4","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1007\/978-1-59745-398-1_25","volume":"484","author":"CB Do","year":"2008","unstructured":"Do CB, Katoh K: Protein multiple sequence alignment. Methods Mol Biol Clifton NJ. 2008, 484: 379-413.","journal-title":"Methods Mol Biol Clifton NJ"},{"key":"6534_CR5","doi-asserted-by":"publisher","first-page":"3073","DOI":"10.1073\/pnas.82.10.3073","volume":"82","author":"M Murata","year":"1985","unstructured":"Murata M, Richardson JS, Sussman JL: Simultaneous comparison of three protein sequences. Proc Natl Acad Sci U S A. 1985, 82: 3073-3077.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"6534_CR6","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. Nucleic Acids Res. 1994, 22: 4673-4680.","journal-title":"Nucleic Acids Res"},{"key":"6534_CR7","doi-asserted-by":"publisher","first-page":"858","DOI":"10.1093\/nar\/gkn1006","volume":"37","author":"T Lassmann","year":"2009","unstructured":"Lassmann T, Frings O, Sonnhammer ELL: Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features. Nucleic Acids Res. 2009, 37: 858-865.","journal-title":"Nucleic Acids Res"},{"key":"6534_CR8","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. Nucleic Acids Res. 2004, 32: 1792-1797.","journal-title":"Nucleic Acids Res"},{"key":"6534_CR9","doi-asserted-by":"publisher","first-page":"615","DOI":"10.1089\/106652701753307511","volume":"8","author":"W Just","year":"2001","unstructured":"Just W: Computational complexity of multiple sequence alignment with SP-score. J Comput Biol J Comput Mol Cell Biol. 2001, 8: 615-623.","journal-title":"J Comput Biol J Comput Mol Cell Biol"},{"key":"6534_CR10","first-page":"85","volume-title":"Proc Eighth Annu Int Conf Res Comput Mol Biol","author":"J Kececioglu","year":"2004","unstructured":"Kececioglu J, Starrett D: Aligning alignments exactly. Proc Eighth Annu Int Conf Res Comput Mol Biol. 2004, New York, NY, USA: ACM, 85-96. RECOMB \u201904,"},{"key":"6534_CR11","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1089\/cmb.1994.1.337","volume":"1","author":"L Wang","year":"1994","unstructured":"Wang L, Jiang T: On the complexity of multiple sequence alignment. J Comput Biol J Comput Mol Cell Biol. 1994, 1: 337-348.","journal-title":"J Comput Biol J Comput Mol Cell Biol"},{"key":"6534_CR12","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1016\/S0304-3975(99)00324-2","volume":"259","author":"P Bonizzoni","year":"2001","unstructured":"Bonizzoni P, Vedova GD: The complexity of multiple sequence alignment with SP-score that is a metric. Theor Comput Sci. 2001, 259: 63-79.","journal-title":"Theor Comput Sci"},{"key":"6534_CR13","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1007\/BF02603120","volume":"25","author":"DF Feng","year":"1987","unstructured":"Feng DF, Doolittle RF: Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J Mol Evol. 1987, 25: 351-360.","journal-title":"J Mol Evol"},{"key":"6534_CR14","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1007\/BF02257378","volume":"20","author":"P Hogeweg","year":"1984","unstructured":"Hogeweg P, Hesper B: The alignment of sets of sequences and the construction of phyletic trees: an integrated method. J Mol Evol. 1984, 20: 175-186.","journal-title":"J Mol Evol"},{"key":"6534_CR15","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1016\/0022-2836(87)90316-0","volume":"198","author":"GJ Barton","year":"1987","unstructured":"Barton GJ, Sternberg MJ: A strategy for the rapid multiple alignment of protein sequences. Confidence levels from tertiary structure comparisons. J Mol Biol. 1987, 198: 327-337.","journal-title":"J Mol Biol"},{"key":"6534_CR16","first-page":"151","volume":"5","author":"DG Higgins","year":"1989","unstructured":"Higgins DG, Sharp PM: Fast and sensitive multiple sequence alignments on a microcomputer. Comput Appl Biosci CABIOS. 1989, 5: 151-153.","journal-title":"Comput Appl Biosci CABIOS"},{"key":"6534_CR17","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9780511790492","volume-title":"Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids","author":"R Durbin","year":"1998","unstructured":"Durbin R, Eddy S, Krogh A, Mitchison G: Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. 1998, Cambridge: University Press"},{"key":"6534_CR18","first-page":"479","volume":"7","author":"MP Berger","year":"1991","unstructured":"Berger MP, Munson PJ: A novel randomized iterative strategy for aligning multiple protein sequences. Comput Appl Biosci CABIOS. 1991, 7: 479-484.","journal-title":"Comput Appl Biosci CABIOS"},{"key":"6534_CR19","first-page":"361","volume":"9","author":"O Gotoh","year":"1993","unstructured":"Gotoh O: Optimal alignment between groups of sequences and its application to multiple sequence alignment. Comput Appl Biosci CABIOS. 1993, 9: 361-370.","journal-title":"Comput Appl Biosci CABIOS"},{"key":"6534_CR20","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-12-144","volume":"12","author":"KM Roskin","year":"2011","unstructured":"Roskin KM, Paten B, Haussler D: Meta-alignment with crumble and prune: partitioning very large alignment problems for performance and parallelization. BMC Bioinformatics. 2011, 12: 1-12.","journal-title":"BMC Bioinformatics"},{"key":"6534_CR21","doi-asserted-by":"publisher","first-page":"705","DOI":"10.1016\/0022-2836(82)90398-9","volume":"162","author":"O Gotoh","year":"1982","unstructured":"Gotoh O: An improved algorithm for matching biological sequences. J Mol Biol. 1982, 162: 705-708.","journal-title":"J Mol Biol"},{"key":"6534_CR22","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1016\/0022-2836(70)90057-4","volume":"48","author":"SB Needleman","year":"1970","unstructured":"Needleman SB, Wunsch CD: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol. 1970, 48: 443-453.","journal-title":"J Mol Biol"},{"key":"6534_CR23","doi-asserted-by":"publisher","first-page":"3356","DOI":"10.1093\/bioinformatics\/btr565","volume":"27","author":"X Ye","year":"2011","unstructured":"Ye X, Wang G, Altschul SF: An assessment of substitution scores for protein profile-profile comparison. Bioinformatics. 2011, 27: 3356-3363.","journal-title":"Bioinformatics"},{"key":"6534_CR24","doi-asserted-by":"publisher","first-page":"396","DOI":"10.1186\/1471-2105-10-396","volume":"10","author":"RC Edgar","year":"2009","unstructured":"Edgar RC: Optimizing substitution matrix choice and gap parameters for sequence alignment. BMC Bioinformatics. 2009, 10: 396.","journal-title":"BMC Bioinformatics"},{"key":"6534_CR25","first-page":"115","volume-title":"Pac Symp Biocomput Pac Symp Biocomput","author":"F Chiaromonte","year":"2002","unstructured":"Chiaromonte F, Yap VB, Miller W: Scoring pairwise genomic sequence alignments. Pac Symp Biocomput Pac Symp Biocomput. 2002, 115-126."},{"key":"6534_CR26","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1186\/1471-2105-5-113","volume":"5","author":"RC Edgar","year":"2004","unstructured":"Edgar RC: MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 2004, 5: 113-doi:10.1186\/1471-2105-5-113","journal-title":"BMC Bioinformatics"},{"key":"6534_CR27","doi-asserted-by":"publisher","first-page":"2433","DOI":"10.1093\/nar\/gki541","volume":"33","author":"PP Gardner","year":"2005","unstructured":"Gardner PP, Wilm A, Washietl S: A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Res. 2005, 33: 2433-2439.","journal-title":"Nucleic Acids Res"},{"key":"6534_CR28","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1186\/1748-7188-1-19","volume":"1","author":"A Wilm","year":"2006","unstructured":"Wilm A, Mainz I, Steger G: An enhanced RNA alignment benchmark for sequence alignment programs. Algorithms Mol Biol. 2006, 1: 19.","journal-title":"Algorithms Mol Biol"},{"key":"6534_CR29","doi-asserted-by":"publisher","first-page":"2648","DOI":"10.1093\/bioinformatics\/btm389","volume":"23","author":"H Carroll","year":"2007","unstructured":"Carroll H, Beckstead W, O\u2019Connor T, Ebbert M, Clement M, Snell Q, McClellan D: DNA reference alignment benchmarks based on tertiary structure of encoded proteins. Bioinformatics. 2007, 23: 2648-2649.","journal-title":"Bioinformatics"},{"key":"6534_CR30","doi-asserted-by":"publisher","first-page":"140","DOI":"10.1186\/1471-2105-5-140","volume":"5","author":"PP Gardner","year":"2004","unstructured":"Gardner PP, Giegerich R: A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics. 2004, 5: 140.","journal-title":"BMC Bioinformatics"},{"key":"6534_CR31","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 Struct Funct Bioinforma. 2005, 61: 127-136.","journal-title":"Proteins Struct Funct Bioinforma"},{"key":"6534_CR32","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1186\/1471-2105-4-47","volume":"4","author":"GPS Raghava","year":"2003","unstructured":"Raghava GPS, Searle SM, Audley PC, Barber JD, Barton GJ: OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy. BMC Bioinformatics. 2003, 4: 47.","journal-title":"BMC Bioinformatics"},{"key":"6534_CR33","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1093\/nar\/27.1.229","volume":"27","author":"CP Ponting","year":"1999","unstructured":"Ponting CP, Schultz J, Milpetz F, Bork P: SMART: identification and annotation of domains from signalling and extracellular protein sequences. Nucleic Acids Res. 1999, 27: 229-232.","journal-title":"Nucleic Acids Res"},{"key":"6534_CR34","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1002\/(SICI)1097-0134(20000701)40:1<6::AID-PROT30>3.0.CO;2-7","volume":"40","author":"JM Sauder","year":"2000","unstructured":"Sauder JM, Arthur JW, Dunbrack RL: Large-scale comparison of protein sequence alignment algorithms with structure alignments. Proteins. 2000, 40: 6-22.","journal-title":"Proteins"},{"key":"6534_CR35","doi-asserted-by":"publisher","first-page":"2682","DOI":"10.1093\/nar\/27.13.2682","volume":"27","author":"JD Thompson","year":"1999","unstructured":"Thompson JD, Plewniak F, Poch O: A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res. 1999, 27: 2682-2690.","journal-title":"Nucleic Acids Res"},{"key":"6534_CR36","doi-asserted-by":"publisher","first-page":"306","DOI":"10.1093\/bioinformatics\/18.2.306","volume":"18","author":"M Cline","year":"2002","unstructured":"Cline M, Hughey R, Karplus K: Predicting reliable regions in protein sequence alignments. Bioinformatics. 2002, 18: 306-314.","journal-title":"Bioinformatics"},{"key":"6534_CR37","doi-asserted-by":"publisher","first-page":"495","DOI":"10.1093\/bioinformatics\/btr701","volume":"28","author":"BP Blackburne","year":"2012","unstructured":"Blackburne BP, Whelan S: Measuring the distance between multiple sequence alignments. Bioinformatics. 2012, 28: 495-502.","journal-title":"Bioinformatics"},{"key":"6534_CR38","doi-asserted-by":"publisher","first-page":"2947","DOI":"10.1093\/bioinformatics\/btm404","volume":"23","author":"MA Larkin","year":"2007","unstructured":"Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG: Clustal W and Clustal X version 2.0. Bioinformatics. 2007, 23: 2947-2948.","journal-title":"Bioinformatics"},{"key":"6534_CR39","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1038\/msb.2011.75","volume":"7","author":"F Sievers","year":"2011","unstructured":"Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, S\u00f6ding J, Thompson JD, Higgins DG: Fast, scalable generation of high\u2012quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011, 7: 539-doi:10.1038\/msb.2011.75","journal-title":"Mol Syst Biol"},{"key":"6534_CR40","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/molbev\/mst010","volume":"30","author":"K Katoh","year":"2013","unstructured":"Katoh K, Standley DM: MAFFT multiple sequence alignment software Version 7: improvements in performance and usability. Mol Biol Evol. 2013, 30: 772-780.","journal-title":"Mol Biol Evol"},{"key":"6534_CR41","doi-asserted-by":"publisher","first-page":"601","DOI":"10.1186\/1471-2105-11-601","volume":"11","author":"DJ Russell","year":"2010","unstructured":"Russell DJ, Way SF, Benson AK, Sayood K: A grammar-based distance metric enables fast and accurate clustering of large sets of 16S sequences. BMC Bioinformatics. 2010, 11: 601.","journal-title":"BMC Bioinformatics"},{"key":"6534_CR42","doi-asserted-by":"publisher","first-page":"330","DOI":"10.1101\/gr.2821705","volume":"15","author":"CB Do","year":"2005","unstructured":"Do CB, Mahabhashyam MSP, Brudno M, Batzoglou S: ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res. 2005, 15: 330-340.","journal-title":"Genome Res"},{"key":"6534_CR43","doi-asserted-by":"publisher","first-page":"e52","DOI":"10.1093\/nar\/gkn174","volume":"36","author":"A Wilm","year":"2008","unstructured":"Wilm A, Higgins DG, Notredame C: R-Coffee: a method for multiple alignment of non-coding RNA. Nucleic Acids Res. 2008, 36: e52.","journal-title":"Nucleic Acids Res"},{"key":"6534_CR44","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: 205-217.","journal-title":"J Mol Biol"},{"key":"6534_CR45","doi-asserted-by":"publisher","first-page":"4917","DOI":"10.1093\/nar\/gkq255","volume":"38","author":"SME Sahraeian","year":"2010","unstructured":"Sahraeian SME, Yoon B-J: PicXAA: greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences. Nucleic Acids Res. 2010, 38: 4917-4928.","journal-title":"Nucleic Acids Res"},{"key":"6534_CR46","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1186\/1748-7188-3-6","volume":"3","author":"AR Subramanian","year":"2008","unstructured":"Subramanian AR, Kaufmann M, Morgenstern B: DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment. Algorithms Mol Biol. 2008, 3: 6.","journal-title":"Algorithms Mol Biol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-15-265.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,23]],"date-time":"2019-01-23T01:02:21Z","timestamp":1548205341000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-15-265"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,8,7]]},"references-count":46,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2014,12]]}},"alternative-id":["6534"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-15-265","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,8,7]]},"assertion":[{"value":"24 March 2014","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 July 2014","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 August 2014","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"265"}}