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

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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

Modules

BioInf
- Alignment
  - BioInf.Alignment.DnaProtein

Downloads

DnaProteinAlignment-0.0.0.1.tar.gz [browse] (Cabal source package)
Package description (as included in the package)

Maintainer's Corner

Package maintainers

ChristianHoener

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Versions [RSS]	0.0.0.1
Change log	changelog
Dependencies	ADPfusion (>=0.2.0.4), ansi-wl-pprint, array, base (>=4 && <5), BiobaseBlast (>=0.0.0.1), BiobaseFasta (>=0.0.1.0), BiobaseXNA (>=0.7.0.2), biocore, bytestring, cmdargs (>=0.10 && <0.11), conduit, dlist, DnaProteinAlignment, parallel, PrimitiveArray (>=0.5.1.0), 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
Distributions
Reverse Dependencies	1 direct, 0 indirect [details]
Executables	DnaProteinAlignment
Downloads	1440 total (0 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]