Frameshift-aware alignment of protein sequences with DNA sequences http://www.tbi.univie.ac.at/~choener/
|Latest on Hackage:||0.0.0.1|
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Perform a semi-global alignment of a DNA sequence (local) with a protein sequence (global). The alignment includes the possibility of frame shifts.
The dynamic programming algorithm is created automatically from atomic single-tape grammars using our grammar product framework.
Run the program with
+RTS -N -RTS for optimal performance
when aligning against a genome.
If you find this library or program useful, please cite:
Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler Product Grammars for Alignment and Folding submitted
Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler How to Multiply Dynamic Programming Algorithms Brazilian Symposium on Bioinformatics (BSB 2013) Lecture Notes in Bioinformatics 8213, Springer, Heidelberg
initial build of the program