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KalignP: Improved multiple sequence alignments using position specific gap penalties in Kalign2
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.ORCID iD: 0000-0002-7115-9751
2011 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 27, no 12, 1702-1703 p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2011. Vol. 27, no 12, 1702-1703 p.
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:su:diva-67549DOI: 10.1093/bioinformatics/btr235ISI: 000291261300019OAI: oai:DiVA.org:su-67549DiVA: diva2:470769
Funder
Swedish Research Council, VR-NT 2009-5072; VR-M 2007-3065EU, FP7, Seventh Framework Programme, 201924Swedish Foundation for Strategic Research
Note

authorCount :2

Available from: 2011-12-29 Created: 2011-12-29 Last updated: 2017-12-08Bibliographically approved

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