BiobaseXNA: Efficient RNA/DNA representations

[ 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 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 (>=0.8 && <1.1), base (>=4.7 && <5.0), bimaps (==0.1.0.*), binary (==0.7.*), BiobaseXNA, bytes (==0.15.*), bytestring (==0.10.*), cereal (>=0.4 && <0.6), cereal-vector (==0.2.*), cmdargs (==0.10.*), containers (==0.5.*), csv (==0.1.*), deepseq (>=1.3 && <1.5), file-embed (>=0.0.8 && <0.1), hashable (==1.2.*), lens (>=4.0 && <5.0), primitive (>=0.5 && <0.7), PrimitiveArray (==0.7.1.*), split (==0.2.*), text (>=1.0 && <1.3), tuple (==0.3.*), vector (>=0.10 && <0.12), vector-binary-instances (==0.2.*), vector-th-unbox (==0.2.*) [details]
License GPL-3.0-only
Copyright Christian Hoener zu Siederdissen, 2011 - 2015
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 repo head: git clone git://github.com/choener/BiobaseXNA
Uploaded by ChristianHoener at Thu Sep 1 23:08:22 UTC 2016
Distributions NixOS:0.10.0.0
Executables SubOptDistance
Downloads 13214 total (78 in the last 30 days)
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Status Docs available [build log]
Last success reported on 2016-10-23 [all 1 reports]
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Readme for BiobaseXNA-0.9.3.0

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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/