Biobase: Base library for bioinformatics

[ bioinformatics, gpl, library ] [ Propose Tags ]

Base library for bioinformatics providing the following features:

RNA sequences and energy files:

  • efficient format for RNA sequences, based on the vector package

  • internal conversion from strings and bytestrings

  • secondary structure manipulation functions, im- and export of Vienna-dotbracket notation

Utility classes:

  • algebraic ring class

  • instances for Gibbs free energy, partition function probabilities, and scores

  • conversion between different entities

Bioinformatics data sources:

  • mostly just imports, some export functions are provided

  • Fasta (please use the "bio" library by Ketil Malde)

  • Mafft

  • RNA secondary structure: Dot-Bracket, CT

  • ViennaRNA energy files (with default parameters)

  • Turner energy files: cf. http://rna.urmc.rochester.edu/NNDB/index.html

  • RNAstrand database: dot-parenthesis (one file, many entries)

  • FR3D: basepairs

  • Infernal: covariance models (text-based)

  • MC-Fold: NCM database

Important notes:

  • In general, this library is not unicode safe (and could somebody tell me the reason for encoding DNA/RNA sequences in unicode?)

Modules

  • Biobase
    • Biobase.Constants
    • DataSource
      • Biobase.DataSource.CT
        • Biobase.DataSource.CT.Import
      • Biobase.DataSource.DotParen
        • Biobase.DataSource.DotParen.Import
      • Biobase.DataSource.FR3D
        • Biobase.DataSource.FR3D.Import
      • Biobase.DataSource.InfernalCM
        • Biobase.DataSource.InfernalCM.Export
        • Biobase.DataSource.InfernalCM.Import
      • Biobase.DataSource.MCFold
        • Biobase.DataSource.MCFold.Conversions
        • Biobase.DataSource.MCFold.Import
      • Biobase.DataSource.Mafft
        • Biobase.DataSource.Mafft.Import
      • Biobase.DataSource.Turner
        • Biobase.DataSource.Turner.Import
        • Biobase.DataSource.Turner.Tables
      • Biobase.DataSource.Vienna
        • Biobase.DataSource.Vienna.Default
        • Export
          • Biobase.DataSource.Vienna.Export.ViennaC
          • Biobase.DataSource.Vienna.Export.ViennaPar
        • Import
          • Biobase.DataSource.Vienna.Import.Turner
          • Biobase.DataSource.Vienna.Import.ViennaPar
        • Modification
          • Biobase.DataSource.Vienna.Modification.NonStandard
          • Biobase.DataSource.Vienna.Modification.Partition
          • Biobase.DataSource.Vienna.Modification.Temperature
    • Biobase.RNA
      • Biobase.RNA.Complex
      • Biobase.RNA.Hashes
      • Biobase.RNA.NucBounds
      • Biobase.RNA.Pairs
      • Biobase.RNA.ViennaPair
    • Biobase.ScoreTypes
    • Biobase.Structure
      • Biobase.Structure.Constraint
      • Biobase.Structure.Shapes
    • Types
      • Biobase.Types.Convert
      • Biobase.Types.Energy
      • Biobase.Types.Partition
      • Biobase.Types.Ring
      • Biobase.Types.Score

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Versions [RSS] 0.0.2.0, 0.0.2.1, 0.1.0.0, 0.1.0.1, 0.3.1.0, 0.3.1.1
Dependencies array, base (>=4 && <5), bytestring, containers, deepseq, directory (>=1), either-unwrap, file-embed (>=0.0.3), filemanip (>=0.3.3 && <0.4), filepath, ghc-prim, HsTools (>=0.0.1.1 && <0.0.2), mtl, parsec (>=3 && <4), ParsecTools (>=0.0.2 && <0.0.3), primitive (>=0.3 && <0.4), PrimitiveArray (>=0.0.3.1 && <0.0.4), split (>=0.1.2.3), tuple (>=0.2.0.1), utility-ht, vector (>=0.7 && <0.8), vector-read-instances, zlib [details]
License GPL-3.0-only
Copyright Christian Hoener zu Siederdissen, 2010,2011
Author Christian Hoener zu Siederdissen
Maintainer choener@tbi.univie.ac.at
Category Bioinformatics
Home page http://www.tbi.univie.ac.at/~choener/
Uploaded by ChristianHoener at 2011-04-08T12:46:37Z
Distributions NixOS:0.3.1.1
Downloads 5921 total (12 in the last 30 days)
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Status Docs not available [build log]
All reported builds failed as of 2016-10-24 [all 15 reports]