BiobaseXNA: Efficient RNA/DNA/Protein Primary/Secondary Structure
This is a base library for bioinformatics with emphasis on RNA and DNA primary structure as well as amino acid sequences.
Provided are efficient encodings for short (limited by the amount of RAM) sequences, as required by RNA folding tools. Extended RNA secondary structures can be represented as well.
Contains data from:
Frequency and isostericity of RNA base pairs Jesse Stombaugh, Craig L. Zirbel, Eric Westhof, and Neocles B. Leontis Nucl. Acids Res. (2009)
http://dx.crossref.org/10.1093%2Fnar%2Fgkp011
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- BiobaseXNA-0.11.1.1.tar.gz [browse] (Cabal source package)
- Package description (as included in the package)
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| Versions [RSS] | 0.5.0.0, 0.5.0.1, 0.5.1.0, 0.5.2.0, 0.5.3.0, 0.5.4.0, 0.5.5.0, 0.5.6.0, 0.6.0.0, 0.6.2.0, 0.6.2.1, 0.6.2.2, 0.6.2.3, 0.6.2.4, 0.6.2.5, 0.6.3.0, 0.6.3.1, 0.7.0.0, 0.7.0.1, 0.7.0.2, 0.8.1.0, 0.8.1.1, 0.8.2.0, 0.8.3.0, 0.9.1.0, 0.9.1.1, 0.9.2.0, 0.9.2.1, 0.9.3.0, 0.9.3.1, 0.10.0.0, 0.11.0.0, 0.11.1.0, 0.11.1.1 (info) |
|---|---|
| Change log | changelog.md |
| Dependencies | aeson (>=1.0), attoparsec (>=0.13), base (>=4.7 && <5.0), bimaps (>=0.1.0 && <0.1.1), binary (>=0.7), BiobaseENA (>=0.0.0 && <0.0.1), BiobaseTypes (>=0.2.1 && <0.2.2), BiobaseXNA, bytes (>=0.15), bytestring (>=0.10), cereal (>=0.4), cereal-vector (>=0.2), cmdargs (>=0.10), containers (>=0.5), csv (>=0.1), data-default (>=0.7), deepseq (>=1.3), DPutils (>=0.1.1 && <0.1.2), file-embed (>=0.0.8), ForestStructures (>=0.0.1 && <0.0.2), hashable (>=1.2), lens (>=4.0), mtl (>=2.0), primitive (>=0.5), PrimitiveArray (>=0.10.1 && <0.10.2), QuickCheck (>=2.7), split (>=0.2), text (>=1.0), tuple (>=0.3), vector (>=0.11), vector-binary-instances (>=0.2), vector-th-unbox (>=0.2) [details] |
| Tested with | ghc ==8.8, ghc ==8.10, ghc ==9.0 |
| License | BSD-3-Clause |
| Copyright | Christian Hoener zu Siederdissen, 2011 - 2021 |
| Author | Christian Hoener zu Siederdissen |
| Maintainer | choener@bioinf.uni-leipzig.de |
| Category | Bioinformatics |
| Home page | https://github.com/choener/BiobaseXNA |
| Bug tracker | https://github.com/choener/BiobaseXNA/issues |
| Source repo | head: git clone git://github.com/choener/BiobaseXNA |
| Uploaded | by ChristianHoener at 2021-06-04T20:20:23Z |
| Distributions | |
| Reverse Dependencies | 17 direct, 2 indirect [details] |
| Executables | SubOptDistance |
| Downloads | 31331 total (107 in the last 30 days) |
| Rating | (no votes yet) [estimated by Bayesian average] |
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| Status | Docs available [build log] Last success reported on 2021-06-04 [all 1 reports] |
Readme for BiobaseXNA-0.11.1.1
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BiobaseXNA
Efficient encoding of (short) biological sequences. This package ist designed to deal with in-memory snippets of DNA, RNA, and amino acids. The encoding is geared toward time-efficiency, not necessarily space efficiency (we use Int's for encoding characters, not the smallest type possible).
Additional modules provide conversion capabilities between different types of characters according to biological laws, and some biochemical constraint information. The latter includes canonical and non-canonical pairing information for RNA.
Actual energy parameters for pairings are provided by other packages, for example BiobaseTurner for the loop energy model with measured parameters.
Contact
Christian Hoener zu Siederdissen
Leipzig University, Leipzig, Germany
choener@bioinf.uni-leipzig.de
http://www.bioinf.uni-leipzig.de/~choener/