{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,26]],"date-time":"2023-01-26T05:20:00Z","timestamp":1674710400181},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1993,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.5"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Kalign2 is one of the fastest and most accurate methods for multiple alignments. However, in contrast to other methods Kalign2 does not allow externally supplied position specific gap penalties. Here, we present a modification to Kalign2, KalignP, so that it accepts such penalties. Further, we show that KalignP using position specific gap penalties obtained from predicted secondary structures makes steady improvement over Kalign2 when tested on Balibase 3.0 as well as on a dataset derived from Pfam-A seed alignments.<\/jats:p>\n               <jats:p>Availability and Implementation: KalignP is freely available at http:\/\/kalignp.cbr.su.se. The source code of KalignP is available under the GNU General Public License, Version 2 or later from the same website.<\/jats:p>\n               <jats:p>Contact: \u00a0arne@bioinfo.se<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr235","type":"journal-article","created":{"date-parts":[[2011,4,20]],"date-time":"2011-04-20T04:06:58Z","timestamp":1303272418000},"page":"1702-1703","source":"Crossref","is-referenced-by-count":6,"title":["KalignP: Improved multiple sequence alignments using position specific gap penalties in Kalign2"],"prefix":"10.1093","volume":"27","author":[{"given":"Nanjiang","family":"Shu","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Biophysics, Stockholm Bioinformatics Center, Center for Biomembrane Research, Swedish e-science Research Center, Stockholm University, 106 91 Stockholm, Sweden"}]},{"given":"Arne","family":"Elofsson","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Biophysics, Stockholm Bioinformatics Center, Center for Biomembrane Research, Swedish e-science Research Center, Stockholm University, 106 91 Stockholm, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2011,4,19]]},"reference":[{"key":"2023012511143590900_B1","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":"2023012511143590900_B2","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":"2023012511143590900_B3","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1006\/jmbi.1999.3091","article-title":"Protein secondary structure prediction based on position-specific scoring matrices","volume":"292","author":"Jones","year":"1999","journal-title":"J. Mol. Biol."},{"key":"2023012511143590900_B4","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1016\/j.jmb.2008.04.052","article-title":"Coils in the membrane core are conserved and functionally important","volume":"380","author":"Kauko","year":"2008","journal-title":"J. Mol. Biol."},{"key":"2023012511143590900_B5","doi-asserted-by":"crossref","first-page":"858","DOI":"10.1093\/nar\/gkn1006","article-title":"Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features","volume":"37","author":"Lassmann","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012511143590900_B6","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1006\/jmbi.2000.4042","article-title":"T-Coffee: a novel method for fast and accurate multiple sequence alignment","volume":"302","author":"Notredame","year":"2000","journal-title":"J. Mol. 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Biol."},{"key":"2023012511143590900_B8","doi-asserted-by":"crossref","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","article-title":"CLUSTAL w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice","volume":"22","author":"Thompson","year":"1994","journal-title":"Nucleic Acids Res."},{"key":"2023012511143590900_B9","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1002\/prot.20527","article-title":"BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark","volume":"61","author":"Thompson","year":"2005","journal-title":"Proteins"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/12\/1702\/48861073\/bioinformatics_27_12_1702.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/12\/1702\/48861073\/bioinformatics_27_12_1702.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T11:14:48Z","timestamp":1674645288000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/12\/1702\/257158"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,4,19]]},"references-count":9,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2011,6,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr235","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,6,15]]},"published":{"date-parts":[[2011,4,19]]}}}