The DnaProteinAlignment package

[Tags:gpl, library, program]

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

Properties

Versions 0.0.0.1
Change log changelog
Dependencies ADPfusion (>=0.2.0.4), ansi-wl-pprint, array, base (==4.*), BiobaseBlast (>=0.0.0.1), BiobaseFasta (>=0.0.1.0), BiobaseXNA (>=0.7.0.2), biocore, bytestring, cmdargs (==0.10.*), conduit, dlist, DnaProteinAlignment, parallel, PrimitiveArray (>=0.5.1.0), repa, split, vector [details]
License GPL-3
Copyright Christian Hoener zu Siederdissen, 2013
Author Christian Hoener zu Siederdissen, 2013
Maintainer choener@tbi.univie.ac.at
Stability experimental
Category Bioinformatics
Home page http://www.tbi.univie.ac.at/~choener/
Source repository head: git clone git://github.com/choener/DnaProteinAlignment
Uploaded Wed Dec 18 00:25:49 UTC 2013 by ChristianHoener
Distributions NixOS:0.0.0.1
Downloads 360 total (3 in the last 30 days)
Votes
0 []
Status Docs not available [build log]
All reported builds failed as of 2015-12-05 [all 5 reports]

Modules

  • BioInf
    • Alignment
      • BioInf.Alignment.DnaProtein

Downloads

Maintainer's Corner

For package maintainers and hackage trustees