estreps: Repeats from ESTs

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Versions [RSS] [faq] 0.1, 0.3, 0.3.1
Dependencies base (>3 && <4), bio (>=0.4), bytestring, containers, random [details]
License LicenseRef-GPL
Author Ketil Malde
Maintainer Ketil Malde <>
Category Bioinformatics
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Uploaded by KetilMalde at 2009-10-07T13:01:48Z
Distributions NixOS:0.3.1
Executables reps, rselect
Downloads 2456 total (20 in the last 30 days)
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For package maintainers and hackage trustees


Readme for estreps-0.3.1

[back to package description]

    rselect - select a random set of sequences from a FASTA file.
    reps    - extract exact k-word repeats based that occur in
              sequences grouped in different clusters.


    You'll need GHC or possibly another Haskell system, and the
    Haskell bioinformatics library.  The Makefile should work to
    build and install (by default to your home directory) the


      rselect [-r] n [m] input.seq

    Selects n sequences from the file input.seq.  If the optional
    m is given, this limits the selection to happen only from the first
    m sequences in the file, which may be more efficient.  If -r is given,
    the sequences will be reoriented randomly.

    The selected sequences are written to standard output, so you
    probably want to redirect them to a file.

      reps k clustered.seq

    Generate a list of repeated k-words (or k-grams) found in the sequences.
    The sequences are expected to be on UniGene format, i.e. a FASTA file
    with #-initiated comments separating the clusters.

    A k-word is considered repeated if it is found in more than one of the

      reps k clustering.lst sequences.seq

    As above, but take a separate input clustering (and ignore any #'s in the
    sequences.  The clustering should consist of one line per cluster, with each
    line containing the sequence identifier (first word after the initial '>'
    in the FASTA header).


    Do let me know about them, at <>!