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.
This library contains BLAST-related functionality:
Parser for tabular NCBI BLAST+ output
Parser for JSON2 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, 0.3.0.0, 0.3.1.0, 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), BiobaseENA (>=0.0.0 && <0.0.1), BiobaseTypes (>=0.2.0 && <0.2.1), BiobaseXNA (>=0.11.0 && <0.11.1), bytestring, cereal (>=0.4), containers, deepseq (>=1.3), directory, file-embed (>=0.0.10), lens (>=4.0), log-domain (>=0.12), mtl (>=2.0), PrimitiveArray (>=0.9.1 && <0.9.2), SciBaseTypes (>=0.1.0 && <0.1.1), text, unordered-containers, vector (>=0.11), vector-th-unbox (>=0.2) [details] |
| License | GPL-3.0-only |
| Copyright | Christian Hoener zu Siederdissen, 2013 - 2019 |
| 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/0.3.1.0(tag 0.3.1.0) |
| Uploaded | by ChristianHoener at 2019-08-28T15:00:56Z |
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- BiobaseBlast-0.3.1.0.tar.gz [browse] (Cabal source package)
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Readme for BiobaseBlast-0.3.1.0
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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/