@hackage DnaProteinAlignment0.0.0.1

Frameshift-aware alignment of protein sequences with DNA sequences

Categories
- Bioinformatics
License
GPL-3.0-only
Maintainer
choener@tbi.univie.ac.at
Links
Versions
- 0.0.0.1 Wed, 18 Dec 2013

Installation
In your cabal file:
Dependencies (17)
- array
- base >=4 && <5
- bytestring
- parallel
- vector
- ADPfusion >=0.2.0.4
Dependents (1)
@hackage/acme-everything

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