Bio::RNA::RNAaliSplit is a distribution of Perl modules for splitting and deconvoluting structural RNA multiple sequence alignments (MSAs). Its primary purpose is to partition a MSA into subsets of sequences that have a common consensus structure which is different from the consesus structure of the other set. Another application is cleaning MSAs from sequence that do not fold into or prohibit folding into a common consensus structure.
This distribution is shipped with a set of executables within the 'scripts' folder. RNAalisplit.pl, takes a RNA MSA in ClustalW format and performs the deconvolution. The eval_alignment.pl executable is a lightweight evaluator for structural alignments of RNA.
This module depends heavily on third party RNA bioinformatics software.
It requires the ViennaRNA Package v2.3.4 or above (available from http://www.tbi.univie.ac.at/RNA ). Specifically, the 'RNAalifold', 'AnalyseDists' executables as well as the RNA Perl module shipped with ViennaRNA are used by RNAaliSplit.
RNAz v2.1 (availale from http://www.tbi.univie.ac.at/~wash/RNAz) is used for classification of split subalignments.
R-scape v1.2.2 or above is used for computing statistically significant covariation in base pairs. Download R-scape from http://www.eddylab.org/R-scape .
Be sure to have all dependencies up and running on your system (and available to the Perl interpreter) prior to installation of Bio::RNA::RNAaliSplit.
To install this module, run the following commands:
perl Makefile.PL
make
make test
make install
After installing, you can find documentation for this module with the perldoc command.
perldoc Bio::RNA::RNAaliSplit
You can also look for information at:
metaCPAN
https://metacpan.org/release/Bio-RNA-RNAaliSplit
RT, CPAN's request tracker (report bugs here)
http://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio-RNA-RNAaliSplit
Copyright (C) 2017-2019 Michael T. Wolfinger ([email protected])
This program is free software; you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
You should have received a copy of the GNU Affero General Public License along with this program. If not, see http://www.gnu.org/licenses/.