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Man Pages
RELIABILITY-PROFILE(1) User Contributed Perl Documentation RELIABILITY-PROFILE(1)

reliability-profile.pl

reliability-profile.pl [options] <locarna-output-dir>

reliability-profile.pl generates a reliability profile plot of a multiple alignment generated by mlocarna --probabilistic.

Brief help message
Full documentation
Project to sequence name
Turn off predicting. (def=on)
Penalty for on/off switching in fit
Position dependent penalty for calculating fit.
Restrict fitting to being exactly once on
Title of plot
Output filename
Offset of sequence in genome
List of (from,to,orientation) triples. Show signals in plot and compared infered signal to them. Give list as string "from0 to0 orientation0;from1 to1 orientation1 ..." Specify multi-range signals by from0a to0a from0b to0b ...
Weight of structure against sequence (1.0)
Weight of the position penalty
Show the influence of structure weight in the plot
Inverse temperature beta
Skip plotting, only output
Write the R script to file
Plot and fit a reverse complement
Write the subsequence of fit
Output format (f = pdf or png, def=pdf)
Show the on/off values for the fit
Uses the file generated by the --consistency command e.g. result.bmreliability-cbt

The target directory of mlocarna is required for obtaining the reliability information. Optionally, the reliability plot will be projected to the sequence with given sequence name (or containing "seqname" as prefix).

2022-11-19 perl v5.32.1

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