{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T23:14:35Z","timestamp":1787008475122,"version":"build-2736575974"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Summary:\u2003We developed PSAR-Align, a multiple sequence realignment tool that can refine a given multiple sequence alignment based on suboptimal alignments generated by probabilistic sampling. Our evaluation demonstrated that PSAR-Align is able to improve the results from various multiple sequence alignment tools.<\/jats:p>\n                  <jats:p>Availability and implementation:\u2003The PSAR-Align source code (implemented mainly in C++) is freely available for download at http:\/\/bioen-compbio.bioen.illinois.edu\/PSAR-Align.<\/jats:p>\n                  <jats:p>Contact:\u2003jbkim@konkuk.ac.kr or jianma@illinois.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt636","type":"journal-article","created":{"date-parts":[[2013,11,12]],"date-time":"2013-11-12T21:59:11Z","timestamp":1384293551000},"page":"1010-1012","source":"Crossref","is-referenced-by-count":16,"title":["PSAR-Align: improving multiple sequence alignment using probabilistic sampling"],"prefix":"10.1093","volume":"30","author":[{"given":"Jaebum","family":"Kim","sequence":"first","affiliation":[{"name":"1 Department of Animal Biotechnology, 2UBITA Center for Biotechnology Research (CBRU), Konkuk University, Seoul 143-701, Korea, 3Department of Bioengineering and 4Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA"},{"name":"1 Department of Animal Biotechnology, 2UBITA Center for Biotechnology Research (CBRU), Konkuk University, Seoul 143-701, Korea, 3Department of Bioengineering and 4Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jian","family":"Ma","sequence":"additional","affiliation":[{"name":"1 Department of Animal Biotechnology, 2UBITA Center for Biotechnology Research (CBRU), Konkuk University, Seoul 143-701, Korea, 3Department of Bioengineering and 4Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA"},{"name":"1 Department of Animal Biotechnology, 2UBITA Center for Biotechnology Research (CBRU), Konkuk University, Seoul 143-701, Korea, 3Department of Bioengineering and 4Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2013,11,12]]},"reference":[{"key":"2023012710451494700_btt636-B1","doi-asserted-by":"crossref","first-page":"e1000392","DOI":"10.1371\/journal.pcbi.1000392","article-title":"Fast statistical alignment","volume":"5","author":"Bradley","year":"2009","journal-title":"PLoS Comput. Biol."},{"key":"2023012710451494700_btt636-B2","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1101\/gr.1960404","article-title":"MAVID: constrained ancestral alignment of multiple sequences","volume":"14","author":"Bray","year":"2004","journal-title":"Genome Res."},{"key":"2023012710451494700_btt636-B3","doi-asserted-by":"crossref","first-page":"iii31","DOI":"10.1093\/bioinformatics\/bti1200","article-title":"DNA assembly with gaps (Dawg): simulating sequence evolution","volume":"21","author":"Cartwright","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012710451494700_btt636-B4","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1101\/gr.2821705","article-title":"ProbCons: probabilistic consistency-based multiple sequence alignment","volume":"15","author":"Do","year":"2005","journal-title":"Genome Res."},{"key":"2023012710451494700_btt636-B5","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012710451494700_btt636-B6","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1093\/nar\/gki198","article-title":"MAFFT version 5: improvement in accuracy of multiple sequence alignment","volume":"33","author":"Katoh","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012710451494700_btt636-B7","doi-asserted-by":"crossref","first-page":"2455","DOI":"10.1093\/bioinformatics\/btp452","article-title":"Upcoming challenges for multiple sequence alignment methods in the high-throughput era","volume":"25","author":"Kemena","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012710451494700_btt636-B8","doi-asserted-by":"crossref","first-page":"6359","DOI":"10.1093\/nar\/gkr334","article-title":"PSAR: measuring multiple sequence alignment reliability by probabilistic sampling","volume":"39","author":"Kim","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012710451494700_btt636-B9","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1101\/gr.5232407","article-title":"Multiple sequence alignment: in pursuit of homologous DNA positions","volume":"17","author":"Kumar","year":"2007","journal-title":"Genome Res."},{"key":"2023012710451494700_btt636-B10","doi-asserted-by":"crossref","first-page":"D64","DOI":"10.1093\/nar\/gks1048","article-title":"The UCSC Genome Browser database: extensions and updates 2013","volume":"41","author":"Meyer","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023012710451494700_btt636-B11","doi-asserted-by":"crossref","first-page":"e123","DOI":"10.1371\/journal.pcbi.0030123","article-title":"Recent evolutions of multiple sequence alignment algorithms","volume":"3","author":"Notredame","year":"2007","journal-title":"PLoS Comput. Biol."},{"key":"2023012710451494700_btt636-B12","doi-asserted-by":"crossref","first-page":"1814","DOI":"10.1101\/gr.076554.108","article-title":"Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs","volume":"18","author":"Paten","year":"2008","journal-title":"Genome Res."},{"key":"2023012710451494700_btt636-B13","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1093\/bioinformatics\/btn630","article-title":"Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment","volume":"25","author":"Paten","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012710451494700_btt636-B14","doi-asserted-by":"crossref","first-page":"R124","DOI":"10.1186\/gb-2007-8-6-r124","article-title":"Measuring the accuracy of genome-size multiple alignments","volume":"8","author":"Prakash","year":"2007","journal-title":"Genome Biol."},{"key":"2023012710451494700_btt636-B15","doi-asserted-by":"crossref","first-page":"2715","DOI":"10.1093\/bioinformatics\/btl472","article-title":"Probalign: multiple sequence alignment using partition function posterior probabilities","volume":"22","author":"Roshan","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012710451494700_btt636-B16","article-title":"Multiple sequence alignment using ClustalW and ClustalX","author":"Thompson","year":"2002","journal-title":"Curr. Protoc. Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/7\/1010\/48922254\/bioinformatics_30_7_1010.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/7\/1010\/48922254\/bioinformatics_30_7_1010.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T06:14:31Z","timestamp":1674800071000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/7\/1010\/232330"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,11,12]]},"references-count":16,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2014,4,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt636","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,4,1]]},"published":{"date-parts":[[2013,11,12]]}}}