BiobaseInfernal: Infernal data structures and tools

[ bioinformatics, gpl, library, program ] [ Propose Tags ]

Provides import and export facilities for Infernal/Rfam data formats. We include Stockholm, CM, verbose Infernal results, and tabulated Infernal results. Some small tools are included.

The VerboseHit format is slightly extended to allow simple annotations. This extension should be backward-compatible with standard-compliant parsers.

This package uses Int's to store sequence position information. Don't compile for 32bit. (And yes, this is a TODO, to change to Int64).

Changes in 0.7.1.0

  • bumped dependencies, compatible to newest BiobaseXNA, PrimitiveArray

Changes in 0.7.0.0

  • work-in-progress release (some features missing)

  • working CM parsing

  • type defns have changed. using phantom types to specify what kind of model we are working with

  • using conduit instead of iteratee

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Versions [RSS] 0.0.2.0, 0.0.2.1, 0.5.0.0, 0.5.1.0, 0.5.2.0, 0.5.3.0, 0.5.3.1, 0.5.4.0, 0.5.4.1, 0.6.0.0, 0.6.0.1, 0.6.2.0, 0.7.0.0, 0.7.0.1, 0.7.1.0, 0.8.1.0
Dependencies attoparsec (>=0.10 && <0.11), attoparsec-conduit (>=0.5 && <0.6), base (>3 && <5), BiobaseXNA (>=0.7 && <0.8), biocore (==0.2), bytestring, bytestring-lexing (>=0.4 && <0.5), conduit (>=0.5 && <0.6), containers, either-unwrap (==1.1), lens (>=3 && <4), primitive (>=0.5), PrimitiveArray (>=0.5 && <0.6), repa (>=3.2 && <3.3), transformers (>=0.3 && <0.4), tuple (>=0.2 && <0.3), vector (>=0.10) [details]
License GPL-3.0-only
Copyright Christian Hoener zu Siederdissen, 2011
Author Christian Hoener zu Siederdissen
Maintainer choener@tbi.univie.ac.at
Category Bioinformatics
Home page http://www.tbi.univie.ac.at/~choener/
Source repo head: git clone git://github.com/choener/BiobaseInfernal
Uploaded by ChristianHoener at 2013-09-20T14:28:00Z
Distributions NixOS:0.8.1.0
Downloads 15202 total (20 in the last 30 days)
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Status Docs uploaded by user
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