title: KalignP: improved multiple sequence alignments using position specific gap penalties in Kalign2.
abstract: CONCLUSIONS
  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.
  
  
  METHODS
  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.
authors.affiliation: Department of Biochemistry and Biophysics, Stockholm Bioinformatics Center, Center for Biomembrane Research, Swedish e-science Research Center, Stockholm University, 106 91 Stockholm, Sweden.
authors.forename: Nanjiang
authors.initials: N
authors.lastname: Shu
authors.forename: Arne
authors.initials: A
authors.lastname: Elofsson
mesh_terms: D017433:Protein Structure, Secondary; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein; D012984:Software