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

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.*), base (>=4.7 && <4.9), bimaps (==0.0.0.*), 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.*), file-embed (==0.0.8.*), hashable (==1.2.*), lens (==4.*), primitive (>=0.5 && <0.7), PrimitiveArray (==0.6.*), split (==0.2.*), text (==1.*), tuple (==0.3.*), vector (==0.10.*), 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 http://www.bioinf.uni-leipzig.de/~choener/
Source repo head: git clone git://github.com/choener/BiobaseXNA
Uploaded by ChristianHoener at Thu May 7 23:50:49 UTC 2015
Distributions NixOS:0.10.0.0
Executables SubOptDistance
Downloads 13714 total (373 in the last 30 days)
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Status Docs not available [build log]
All reported builds failed as of 2016-12-09 [all 7 reports]
Hackage Matrix CI

Modules

  • Biobase
    • Biobase.Primary
      • Biobase.Primary.AA
      • Biobase.Primary.Hashed
      • Biobase.Primary.IUPAC
      • Biobase.Primary.Letter
      • Biobase.Primary.Nuc
        • Biobase.Primary.Nuc.Conversion
        • Biobase.Primary.Nuc.DNA
        • Biobase.Primary.Nuc.RNA
        • Biobase.Primary.Nuc.XNA
      • Biobase.Primary.Trans
    • Biobase.Secondary
      • Biobase.Secondary.Basepair
      • Biobase.Secondary.Constraint
      • Biobase.Secondary.Diagrams
      • Biobase.Secondary.Isostericity
      • Biobase.Secondary.Pseudoknots
      • Biobase.Secondary.Structure
      • Biobase.Secondary.Vienna

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