@hackage Biobase0.1.0.1

Base library for bioinformatics

  • Installation

  • Dependencies (0)

  • Dependents (0)

Base library for bioinformatics providing the following features:

  • RNA primary and secondary structure

  • Infernal covariance models

  • Turner and Vienna energy files

RNA sequences and energy files:

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

  • import from strings, bytestrings, fasta files (using the bio library)

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

  • import Turner energy files

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

  • im- and export of Vienna 2.0 energy files

Covariance models:

  • import covariance models

  • basic manipulation of covariance models

  • Stockholm file format manipulation

Utility classes:

  • algebraic ring class

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

  • conversion between different entities

  • ready for the vector library