KalignP: Improved multiple sequence alignments using position
specific gap penalties in Kalign2
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KalignP is a modification to Kalign2, so that it accepts externally
supplied position specific gap penalties. 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 of derived from
Pfam-A seed alignments. Further, KalignP is more flexible than
Kalign2, as researchers can modify the behavior of alignment using
other knowledge.
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References |
Nanjiang Shu and Arne Elofsson. KalignP: Improved multiple sequence alignments using position specific gap penalties in Kalign2. Bioinformatics, 2011;27(12):1702-3 |
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