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

Version0.0.0.1
DependenciesADPfusion (>=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
LicenseGPL-3
CopyrightChristian Hoener zu Siederdissen, 2013
AuthorChristian Hoener zu Siederdissen, 2013
Maintainerchoener@tbi.univie.ac.at
Stabilityexperimental
CategoryBioinformatics
Home pagehttp://www.tbi.univie.ac.at/~choener/
Source repositoryhead: git clone git://github.com/choener/DnaProteinAlignment
ExecutablesDnaProteinAlignment
UploadedWed Dec 18 00:25:49 UTC 2013 by ChristianHoener
Downloads165 total (13 in last 30 days)
StatusDocs not available [build log]
All reported builds failed [all 1 reports]

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