Journal Article

KalignP: Improved multiple sequence alignments using position specific gap penalties in Kalign2

Nanjiang Shu and Arne Elofsson

in Bioinformatics

Volume 27, issue 12, pages 1702-1703
Published in print June 2011 | ISSN: 1367-4803
Published online April 2011 | e-ISSN: 1460-2059 | DOI:

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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.

Availability and Implementation: KalignP is freely available at The source code of KalignP is available under the GNU General Public License, Version 2 or later from the same website.


Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1406 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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