Base library for bioinformatics

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GPL-3.0-only licensed by Christian Hoener zu Siederdissen

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.

  • 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?)

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