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 0.6.0.0

Changes in 0.5.4.1

Versions [faq] 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, attoparsec-iteratee, base (>3 && <5), biocore, bytestring, containers, either-unwrap, iteratee, iteratee-compress, PrimitiveArray, transformers, tuple, vector [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/
Uploaded by ChristianHoener at Wed Nov 30 14:03:07 UTC 2011
Distributions NixOS:0.8.1.0
Downloads 10626 total (192 in the last 30 days)
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Status Hackage Matrix CI
Docs not available [build log]
All reported builds failed as of 2016-12-26 [all 8 reports]

Modules

  • Biobase
    • Biobase.Infernal
      • Biobase.Infernal.CM
        • Biobase.Infernal.CM.Export
        • Biobase.Infernal.CM.Import
      • Biobase.Infernal.Clan
        • Biobase.Infernal.Clan.Import
      • Biobase.Infernal.Hit
      • Biobase.Infernal.RfamFasta
        • Biobase.Infernal.RfamFasta.Import
      • Biobase.Infernal.TabularHit
        • Biobase.Infernal.TabularHit.Import
      • Biobase.Infernal.Taxonomy
        • Biobase.Infernal.Taxonomy.Import
      • Biobase.Infernal.Types
      • Biobase.Infernal.VerboseHit
        • Biobase.Infernal.VerboseHit.Export
        • Biobase.Infernal.VerboseHit.Import
        • Biobase.Infernal.VerboseHit.Internal

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