@hackage Biobase0.1.0.1

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