rMSA

rMSA (RNA Multiple Sequence Alignment) is an automated pipeline to search and align homologs from RNAcentral and nt databases for a target RNA.

Install

git clone https://github.com/pylelab/rMSA
cd rMSA
./database/script/update.sh    # Download RNAcentral and nt

All 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.

Third party programs

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.

Run the program

./rMSA.pl seq.fasta

Run ./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.

License

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.

Citation

Chengxin Zhang, Yang Zhang, Anna Marie Pyle (2022) rMSA: a sequence search and alignment algorithm to improve RNA structure modeling. J Mol Biol. 167904.