MOUNTAIN

NAME

    mountain − produce coordinates for a mountain plot from a dot plot

SYNOPSIS

    mountain.pl myseq_dp.ps > mountain.dat

DESCRIPTION

    reads pair proabilities and MFE structure from a probability dot
    plot as produced by C<RNAfold −p>, and produces x−y data suitable
    for producing a mountain plot using standard xy−plotting programs.
    Output consists of 3 data sets separated by a line containing only
    the C<&> character. The first two sets are mountain representations
    computed from base pair probabilities and mfe structure, respectively.
    For the mfe case the moutain plot graphs the number base pairs
    enclosing a position k, in case of pair probabilities we use the average
    number of base pairs computed as m_k = \Sum_i<k<j p_ij.
    The third set contains the positional entropy, which provides a measure
    of local structural welldefinedness, s_i = −\Sum_j p_ij * ln(p_ij).
    The output is suitable for graphing with xmgrace, e.g.:
    C< RNAfold −p < foo.seq; mountain.pl foo_dp.ps | xmgrace −pipe>

AUTHOR

Ivo L. Hofacker <ivo@tbi.univie.ac.at>