name: DnaProteinAlignment
version: 0.0.0.1
author: Christian Hoener zu Siederdissen, 2013
copyright: Christian Hoener zu Siederdissen, 2013
homepage: http://www.tbi.univie.ac.at/~choener/
maintainer: choener@tbi.univie.ac.at
category: Bioinformatics
license: GPL-3
license-file: LICENSE
build-type: Simple
stability: experimental
cabal-version: >= 1.8.0
synopsis:
Frameshift-aware alignment of protein sequences with DNA sequences
description:
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
@
Extra-Source-Files:
BioInf/Alignment/DnaProtein.gra
changelog
library
build-depends:
ansi-wl-pprint ,
base >= 4 && < 5 ,
cmdargs == 0.10.* ,
ADPfusion >= 0.2.0.4 ,
array ,
BiobaseBlast >= 0.0.0.1 ,
BiobaseFasta >= 0.0.1.0 ,
BiobaseXNA >= 0.7.0.2 ,
biocore ,
bytestring ,
conduit ,
dlist ,
parallel ,
PrimitiveArray >= 0.5.1.0 ,
repa ,
split ,
vector
exposed-modules:
BioInf.Alignment.DnaProtein
ghc-options:
-O2
-fllvm
-fsimpl-tick-factor=1000
executable DnaProteinAlignment
build-depends:
ansi-wl-pprint ,
base >= 4 && < 5 ,
cmdargs == 0.10.* ,
ADPfusion >= 0.2.0.4 ,
array ,
BiobaseBlast >= 0.0.0.1 ,
BiobaseFasta >= 0.0.1.0 ,
BiobaseXNA >= 0.7.0.2 ,
biocore ,
bytestring ,
conduit ,
dlist ,
DnaProteinAlignment ,
parallel ,
PrimitiveArray >= 0.5.1.0 ,
repa ,
split ,
vector
ghc-options:
-O2
-fllvm
-fsimpl-tick-factor=1000
-threaded
-rtsopts
main-is:
DnaProteinAlignment.hs
source-repository head
type: git
location: git://github.com/choener/DnaProteinAlignment