DnaProteinAlignment: Frameshift-aware alignment of protein sequences with DNA sequences

[ bioinformatics, gpl, library, program ] [ Propose Tags ]

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
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


  • BioInf
    • Alignment
      • BioInf.Alignment.DnaProtein


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Change log changelog
Dependencies ADPfusion (>=, ansi-wl-pprint, array, base (>=4 && <5), BiobaseBlast (>=, BiobaseFasta (>=, BiobaseXNA (>=, biocore, bytestring, cmdargs (>=0.10 && <0.11), conduit, dlist, DnaProteinAlignment, parallel, PrimitiveArray (>=, repa, split, vector [details]
License GPL-3.0-only
Copyright Christian Hoener zu Siederdissen, 2013
Author Christian Hoener zu Siederdissen, 2013
Maintainer choener@tbi.univie.ac.at
Category Bioinformatics
Home page http://www.tbi.univie.ac.at/~choener/
Source repo head: git clone git://github.com/choener/DnaProteinAlignment
Uploaded by ChristianHoener at 2013-12-18T00:25:49Z
Reverse Dependencies 1 direct, 0 indirect [details]
Executables DnaProteinAlignment
Downloads 1421 total (8 in the last 30 days)
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Status Docs not available [build log]
All reported builds failed as of 2016-10-25 [all 15 reports]