KalignP: Improved multiple sequence alignments using position specific gap penalties in Kalign2
2011 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1460-2059, Vol. 27, no 12, 1702-1703 p.Article in journal (Refereed) Published
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.
IdentifiersURN: urn:nbn:se:su:diva-67549DOI: 10.1093/bioinformatics/btr235ISI: 000291261300019OAI: oai:DiVA.org:su-67549DiVA: diva2:470769
FunderSwedish Research Council, VR-NT 2009-5072; VR-M 2007-3065EU, FP7, Seventh Framework Programme, 201924Swedish Foundation for Strategic Research
authorCount :22011-12-292011-12-292014-11-10Bibliographically approved