# 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>