The Biobase package
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?)
Properties
| Versions | 0.0.2.0, 0.0.2.1, 0.1.0.0, 0.1.0.1, 0.3.1.0, 0.3.1.1 |
|---|---|
| Dependencies | array, base (4.*), bytestring, containers, deepseq, directory (≥1), either-unwrap, file-embed (≥0.0.3), filemanip (≥0.3.3 & <0.4), filepath, ghc-prim, HsTools (≥0.0.1.1 & <0.0.2), mtl, parsec (3.*), ParsecTools (0.0.2.*), primitive (0.3.*), PrimitiveArray (≥0.0.3.1 & <0.0.4), split (≥0.1.2.3), tuple (≥0.2.0.1), utility-ht, vector (0.7.*), vector-read-instances, zlib |
| License | GPL-3 |
| Copyright | Christian Hoener zu Siederdissen, 2010,2011 |
| Author | Christian Hoener zu Siederdissen |
| Maintainer | choener@tbi.univie.ac.at |
| Stability | experimental |
| Category | Bioinformatics |
| Home page | http://www.tbi.univie.ac.at/~choener/ |
| Upload date | Fri Apr 8 12:46:37 UTC 2011 |
| Uploaded by | ChristianHoener |
| Build failure | ghc-7.0 (log) |
Modules
- Biobase
- Biobase.Constants
- DataSource
- Biobase.DataSource.CT
- Biobase.DataSource.CT.Import
- Biobase.DataSource.DotParen
- Biobase.DataSource.DotParen.Import
- Biobase.DataSource.FR3D
- Biobase.DataSource.FR3D.Import
- Biobase.DataSource.InfernalCM
- Biobase.DataSource.InfernalCM.Export
- Biobase.DataSource.InfernalCM.Import
- Biobase.DataSource.MCFold
- Biobase.DataSource.MCFold.Conversions
- Biobase.DataSource.MCFold.Import
- Biobase.DataSource.Mafft
- Biobase.DataSource.Mafft.Import
- Biobase.DataSource.Turner
- Biobase.DataSource.Turner.Import
- Biobase.DataSource.Turner.Tables
- Biobase.DataSource.Vienna
- Biobase.DataSource.Vienna.Default
- Export
- Biobase.DataSource.Vienna.Export.ViennaC
- Biobase.DataSource.Vienna.Export.ViennaPar
- Import
- Biobase.DataSource.Vienna.Import.Turner
- Biobase.DataSource.Vienna.Import.ViennaPar
- Modification
- Biobase.DataSource.Vienna.Modification.NonStandard
- Biobase.DataSource.Vienna.Modification.Partition
- Biobase.DataSource.Vienna.Modification.Temperature
- Biobase.DataSource.CT
- Biobase.RNA
- Biobase.RNA.Complex
- Biobase.RNA.Hashes
- Biobase.RNA.NucBounds
- Biobase.RNA.Pairs
- Biobase.RNA.ViennaPair
- Biobase.ScoreTypes
- Biobase.Structure
- Biobase.Structure.Constraint
- Biobase.Structure.Shapes
- Types
- Biobase.Types.Convert
- Biobase.Types.Energy
- Biobase.Types.Partition
- Biobase.Types.Ring
- Biobase.Types.Score
Downloads
- Biobase-0.3.1.1.tar.gz (Cabal source package)
- package description (included in the package)