KalignP: improved multiple sequence alignments using position specific gap penalties in Kalign2.
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ABSTRACT: 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 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.
SUBMITTER: Shu N
PROVIDER: S-EPMC3106193 | biostudies-literature | 2011 Jun
REPOSITORIES: biostudies-literature
Publications
KalignP: improved multiple sequence alignments using position specific gap penalties in Kalign2.
Shu Nanjiang N Elofsson Arne A
Bioinformatics (Oxford, England) 20110419 12
<h4>Summary</h4>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 datase ...[more]
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