BiobaseBlast: BLAST-related tools

[ bioinformatics, gpl, library ] [ Propose Tags ]

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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Versions [RSS] 0.0.0.1, 0.2.0.0, 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), BiobaseENA (>=0.0.0 && <0.0.1), BiobaseTypes (>=0.2.1 && <0.2.2), BiobaseXNA (>=0.11.1 && <0.11.2), 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 (>=0.10.1 && <0.10.2), SciBaseTypes (>=0.1.1 && <0.1.2), 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 FlorianEggenhofer at 2021-06-05T21:06:10Z
Distributions NixOS:0.3.3.0
Downloads 4000 total (20 in the last 30 days)
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Status Docs available [build log]
Last success reported on 2021-06-05 [all 1 reports]

Readme for BiobaseBlast-0.3.3.0

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BiobaseBlast Hackage github action: CI

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/