The BiobaseXNA package

[Tags: gpl, library, program]

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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Versions0.5.0.0, 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 (info)
Change logchangelog.md
Dependenciesaeson (>=0.8 && <0.11), base (>=4.7 && <4.9), bimaps (>=0.0.0.2 && <0.0.1.0), binary (==0.7.*), 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 && <1.5), file-embed (>=0.0.8 && <0.0.10), hashable (==1.2.*), lens (>=4.0 && <4.14), primitive (>=0.5 && <0.7), PrimitiveArray (==0.7.0.*), 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]
LicenseGPL-3
CopyrightChristian Hoener zu Siederdissen, 2011 - 2015
AuthorChristian Hoener zu Siederdissen
Maintainerchoener@bioinf.uni-leipzig.de
Stabilityexperimental
CategoryBioinformatics
Home pagehttps://github.com/choener/BiobaseXNA
Bug trackerhttps://github.com/choener/BiobaseXNA/issues
Source repositoryhead: git clone git://github.com/choener/BiobaseXNA
ExecutablesSubOptDistance
UploadedSun Nov 22 16:05:14 UTC 2015 by ChristianHoener
Downloads6674 total (70 in last 30 days)
Votes
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StatusDocs available [build log]
Last success reported on 2015-12-05 [all 3 reports]

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For package maintainers and hackage trustees

Readme for BiobaseXNA-0.9.2.1

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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/