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Thread: New test profile: hmmer

  1. #1
    Join Date
    Apr 2008
    Location
    York, UK
    Posts
    134

    Default New test profile: hmmer

    Hmmer is a computational biology tool for creating and searching profile hidden markov models of biological sequence data. This test performs a timed search on the Pfam database looking for the domain structure of a particular protein sequence.
    Note this test requires a large amount of environment disk space (>700MB) as the entire Pfam sequence database needs to be downloaded and decompressed.

    This profile may be expanded in the future to test more of the functionality of hmmer such as building and calibrating models.

    Test: http://fire-salamander.co.uk/pts-tes...er-0.3.tar.bz2

    Refs:
    hmmer - http://hmmer.janelia.org/
    Pfam - http://pfam.sanger.ac.uk/

  2. #2

    Default

    Will be in git shortly, thanks! Also, is this supposed to be part of the molecular dynamics suite?

  3. #3
    Join Date
    Apr 2008
    Location
    York, UK
    Posts
    134

    Default

    No. Once I've finished the other profile I'm creating, I'll create a new comp-biol suite that will run tests from all 3 profiles.

    For the time being md-gromacs will be the only test run in the molecular dynamics suite, unless I can find other software packages with free licenses.

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