@hackage Biobase0.3.1.1

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?)