The BiobaseXNA package

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

This is a base library for bioinformatics with emphasis on RNA and DNA primary structure as well as amino acid sequences.

Provided are efficient encodings for short (limited by the amount of RAM) sequences, as required by RNA folding tools. Extended RNA secondary structures can be represented as well.

Contains data from:

Frequency and isostericity of RNA base pairs
Jesse Stombaugh, Craig L. Zirbel, Eric Westhof, and Neocles B. Leontis
Nucl. Acids Res. (2009)

http://dx.crossref.org/10.1093%2Fnar%2Fgkp011


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Versions 0.5.0.0, 0.5.0.1, 0.5.1.0, 0.5.2.0, 0.5.3.0, 0.5.4.0, 0.5.5.0, 0.5.6.0, 0.6.0.0, 0.6.2.0, 0.6.2.1, 0.6.2.2, 0.6.2.3, 0.6.2.4, 0.6.2.5, 0.6.3.0, 0.6.3.1, 0.7.0.0, 0.7.0.1, 0.7.0.2, 0.8.1.0, 0.8.1.1, 0.8.2.0, 0.8.3.0, 0.9.1.0, 0.9.1.1, 0.9.2.0, 0.9.2.1, 0.9.3.0, 0.9.3.1, 0.10.0.0 (info)
Change log changelog.md
Dependencies aeson (>=1.0), attoparsec (>=0.13), base (>=4.7 && <5.0), bimaps (==0.1.0.*), binary (>=0.7), BiobaseTypes (==0.1.3.*), BiobaseXNA, bytes (>=0.15), bytestring (>=0.10), cereal (>=0.4), cereal-vector (>=0.2), cmdargs (>=0.10), containers (>=0.5), csv (>=0.1), deepseq (>=1.3), file-embed (>=0.0.8), ForestStructures (==0.0.0.*), hashable (>=1.2), lens (>=4.0), mtl (>=2.0), primitive (>=0.5), PrimitiveArray (==0.8.0.*), QuickCheck (>=2.7), split (>=0.2), text (>=1.0), tuple (>=0.3), vector (>=0.10), vector-binary-instances (>=0.2), vector-th-unbox (>=0.2) [details]
License GPL-3
Copyright Christian Hoener zu Siederdissen, 2011 - 2017
Author Christian Hoener zu Siederdissen
Maintainer choener@bioinf.uni-leipzig.de
Category Bioinformatics
Home page https://github.com/choener/BiobaseXNA
Bug tracker https://github.com/choener/BiobaseXNA/issues
Source repository head: git clone git://github.com/choener/BiobaseXNA
Uploaded Thu Nov 23 22:08:51 UTC 2017 by ChristianHoener
Distributions NixOS:0.10.0.0
Executables SubOptDistance
Downloads 9775 total (1029 in the last 30 days)
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Status Docs available [build log]
Last success reported on 2017-11-23 [all 1 reports]
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Readme for BiobaseXNA-0.10.0.0

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BiobaseXNA

Efficient encoding of (short) biological sequences. This package ist designed to deal with in-memory snippets of DNA, RNA, and amino acids. The encoding is geared toward time-efficiency, not necessarily space efficiency (we use Int's for encoding characters, not the smallest type possible).

Additional modules provide conversion capabilities between different types of characters according to biological laws, and some biochemical constraint information. The latter includes canonical and non-canonical pairing information for RNA.

Actual energy parameters for pairings are provided by other packages, for example BiobaseTurner for the loop energy model with measured parameters.

Contact

Christian Hoener zu Siederdissen
Leipzig University, Leipzig, Germany
choener@bioinf.uni-leipzig.de
http://www.bioinf.uni-leipzig.de/~choener/