rMSA (RNA Multiple Sequence Alignment) is an automated pipeline to search and align homologs from RNAcentral and nt databases for a target RNA.
git clone https://github.com/kad-ecoli/rMSA
cd rMSA
./database/script/update.sh # Download RNAcentral and ntAll precompiled binaries in the rMSA package are for 64bit Linux (x86-64) only.
For other operating systems, you need to compile the rMSA ultilities using
src/Makefile, and other thrid-party programs listed below.
The bin folder includes binaries precompiled for 64bit Linux for
the following programs.
- nhmmer (
bin/qnhmmer) from HMMER 3.3 - cd-hit-est and cd-hit-est-2d from CD-HIT 4.8.1
- clustalo 1.2.4
- cmbuild, cmcalibrate, cmscan and cmsearch (
bin/qcmsearch) from INFERNAL 1.1.3 - hhfilter and reformat.pl from HH-suite 2.0.15
- RNAfold from ViennaRNA 2.4.14
- dot2ct from RNAstructure 6.2
- plmc 2018-05-16
The output format of nhmmer and cmsearch are modifed from
eslMSAFILE_STOCKHOLM or eslMSAFILE_PFAM to eslMSAFILE_A2M.
./rMSA.pl seq.fastaRun ./rMSA.pl without command line argument to get full option list,
including alternative databases, temporary folders, number of CPU threads
(default is 1) and the secondary structure. Nucleotide U is converted to T.
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.