NAME

eval_alignment.pl - A structural alignment evaluator

SYNOPSIS

eval_alignment.pl [--aln|-a FILE] [-out|-o DIR] [--log|-l FILE] [--statistic|-s STRING] [--nofigures] [options]

DESCRIPTION

This is a semi-automatic evaluator for RNA alignemnts. In employs R-scape (http://eddylab.org/R-scape/) and RNAz (https://www.tbi.univie.ac.at/software/RNAz) to classify structural RNA alignments. It accepts a single multiple sequence alignment in Stockholm format and runs R-scape and RNAz on it, determining statistically significant covarying base pairs (SSCBP) and RNAz classification parameters.

This tool prints the RNAz class probability, the applied R-scape covariance statistic, the number of SSCBP, the lenth of the alignment, as well as the number of base pairs and sequences to stdout. R-scapoe and RNAz output files are written to a user-defined directory.

DISCLAIMER

This script employs a simple R-scape/RNAz warpper. As such, it does not implement (and pass through) all R-scape/RNAz options.

Please ensure that R-scape >v0.6.1 is installed on your machine and available for your Perl interpreter.

OPTIONS

--aln|-a

A multiple sequence alignment in Stockholm format.

--statistic|-s

The covariation statistic used by R-scape. Allowed values are: 'GT', 'MI', 'MIr', 'MIg', 'CHI', 'OMES', 'RAF', 'RAFS'. Appending either 'p' or 'a' to any of them calculates its average product correction and average sum correction, respctively (e.g. GTp or GTa). See the R-scape manual for details.

--nofigures|-n

Turn off production of graphical R-scape output

--log|-l

Specify log file; output is written to STDOUT unless specified

--version

Show wrap-R-scape.pl version and exit

SEE ALSO

The R-scape manual and the R-scape paper.

AUTHOR

Michael T. Wolfinger <michael@wolfinger.eu> and <michael.wolfinger@univie.ac.at>