KalignP: Improved multiple sequence alignments using position specific gap penalties in Kalign2
Tuesday, November 4 2025
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KalignP: Improved multiple sequence alignments using position specific gap penalties in Kalign2
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.
 
Enter sequences in Enhanced FASTA format

Alternatively, upload a text file containing sequences in Enhanced FASTA format
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Add position specific gap penalties from secondary structures predicted by PSIPRED (using single sequence). If the position specific gap penalties are already supplied in the FASTA sequence file, it will not be run.
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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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