@hackage BiobaseBlast0.2.0.0

BLAST-related tools

Categories
- Bioinformatics
License
GPL-3.0-only
Maintainer
choener@bioinf.uni-leipzig.de
Links
Versions
- 0.3.3.0 Sat, 5 Jun 2021
- 0.3.1.0 Wed, 28 Aug 2019
- 0.3.0.0 Fri, 14 Jun 2019
- 0.2.1.0 Thu, 28 Sep 2017
- 0.2.0.0 Fri, 7 Jul 2017
- 0.0.0.1 Fri, 6 Dec 2013

Installation
In your cabal file:
Tested Compilers
- 8.0.2
- 7.10.3
Dependencies (14)
- base >=4.7 && <5.0
- binary >=0.7
- bytestring
- containers
- deepseq >=1.3
- directory
Dependents (4)
@hackage/RNAlien, @hackage/DnaProteinAlignment, @hackage/acme-everything, @hackage/BlastHTTP

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/