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1. Installation
    Requirements: Linux OS, g++ compiler 4.7.2 or later, you may have
    to modify Makefile if your default compiler is outdated.
    unzip MotifFinder.zip
    cd MotifFinder
    make
2. Running motifFinder.exe (MF)
    Execute MF without arguments for usage information.
3. Input format.
    Input directory is suplied as first argument to MF. This directory contains
    text files with extension .txt, files not having this extension will be ignored.
    Each file should contain one sequence of nucleotides with
    exons delimeted by "XXX". After splitting read sequences, 
    all substrings shorter than 50 nucleotides are discarded. 
4. Algorithm.
    MF will consider all available string of nucleotides of length 50,
    search for motifs in the first 15 nucleotides of a string (front subsequence),
    then augment found front motifs by searching for motifs in the last 15 
    nucleotides (tail subsequence), 20 nucleotides in the middle do not matter.
    Maximum number of mismatches is specified in the second argument,
    this constrain must be satisfied by each front and each tail sequence.
    MF will record and output all motifs observed in no fewer than N 
    sequences (files), where N is MF's third argument. Nucleotide "A" is 
    assumed to be equivalent to nucleotide "G".
5. Output.
    The following files are created in the working directory.
    MotifFinder.log containing progress updates. 
    Motifs.output containing two tab delimeted fields: 
        - number of matched sequences (score),
        - motif given as (front sequence).(tail sequence), "." stands for 
          middle 20 characters.
    Since nucleotides "A" and "G" are equivalent, each motif will contain only the one 
    most frequently observed during matching.
    Motifs.output.detail containing these "|" delimeted fields
        - number of matched sequences (score),
        - motif given as (front sequence).(tail sequence), "." stands for 
          middle 20 characters.
        - vector of scores for each nucleotide in the front sequence.
        - vector of scores for each nucleotide in the tail sequence.
        - vector with number of mismatches for motif's front sequence.
        - vector with number of mismatches for motif's tail sequence.
6. Design
    aux.* contains a few utility functions.
    BioSeq.* implements containers for sequences, motifs, as well as 
    search functions.
    mf.cpp is main function.