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

  • multiple changes to data representation (mostly newtypes) and documentation

  • load the Rfam.fasta.gz file (and prepare lookup structures)

  • partial biocore integration

Changes in 0.5.4.1

  • fix-up for VH export

  • half-baked CM type (not useful yet)

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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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, 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 2011-11-30T14:03:07Z
Distributions NixOS:0.8.1.0
Downloads 15202 total (20 in the last 30 days)
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Status Docs not available [build log]
All reported builds failed as of 2016-12-26 [all 8 reports]