BiobaseBlast: BLAST-related tools
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Warnings:
- 'ghc-options: -O2' is rarely needed. Check that it is giving a real benefit and not just imposing longer compile times on your users.
- Exposed modules use unallocated top-level names: Biobase
This library contains BLAST-related functionality:
Parser for tabular NCBI BLAST+ output
Parsers for BLOSUM and PAM matrices.
Specialized substitution functions for (in)complete amino acid / nucleotide triplet substitution.
Incomplete nucleotide patterns map one or two nucleotides to an amino acid (need for indel editing in the mitochondria of certain species like p.polycephalum).
The matrices are currently not provided but can be found here: ftp://ftp.ncbi.nih.gov/blast/matrices/
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Properties
| Versions | 0.0.0.1, 0.2.0.0, 0.2.1.0, 0.2.1.0, 0.3.0.0, 0.3.1.0, 0.3.3.0 |
|---|---|
| Change log | changelog.md |
| Dependencies | aeson (>=1.0), attoparsec (>=0.13), base (>=4.7 && <5.0), binary (>=0.7), BiobaseTypes (>=0.1.2 && <0.1.3), BiobaseXNA (>=0.9.3 && <0.9.4), bytestring, cereal (>=0.4), containers, deepseq (>=1.3), directory, PrimitiveArray (>=0.8.0 && <0.8.1), vector (>=0.10), vector-th-unbox (>=0.2) [details] |
| License | GPL-3.0-only |
| Copyright | Christian Hoener zu Siederdissen, 2013 - 2017 |
| Author | Christian Hoener zu Siederdissen, Florian Eggenhofer |
| Maintainer | choener@bioinf.uni-leipzig.de |
| Category | Bioinformatics |
| Home page | https://github.com/choener/BiobaseBlast |
| Bug tracker | https://github.com/choener/BiobaseBlast/issues |
| Source repo | head: git clone https://github.com/choener/BiobaseBlast this: git clone https://github.com/choener/BiobaseBlast/tree/0.2.1.0(tag 0.2.1.0) |
| Uploaded | by ChristianHoener at 2017-09-28T14:59:48Z |
Modules
- Biobase
- Biobase.BLAST
- Biobase.BLAST.Import
- Biobase.BLAST.Types
- Biobase.SubstMatrix
- Biobase.SubstMatrix.Import
- Biobase.BLAST
Downloads
- BiobaseBlast-0.2.1.0.tar.gz [browse] (Cabal source package)
- Package description (as included in the package)
Maintainer's Corner
Package maintainers
For package maintainers and hackage trustees
Readme for BiobaseBlast-0.2.1.0
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BiobaseBlast
This library contains BLAST-related functionality.
Contact
Christian Hoener zu Siederdissen
Leipzig University, Leipzig, Germany
choener@bioinf.uni-leipzig.de
http://www.bioinf.uni-leipzig.de/~choener/