Biobase
Version 0.3.1.1 revision 0 uploaded by ChristianHoener.
Package meta
- Synopsis
- Base library for bioinformatics
- Description
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?)
- Author
- Christian Hoener zu Siederdissen
- Bug reports
- n/a
- Category
- Bioinformatics
- Copyright
- Christian Hoener zu Siederdissen, 2010,2011
- Homepage
- http://www.tbi.univie.ac.at/~choener/
- Maintainer
- choener@tbi.univie.ac.at
- Package URL
- n/a
- Stability
- experimental