Shunsuke-1994 / rMSA2

RNA Multiple Sequence Alignment

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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/kad-ecoli/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
  • PETfold 2.1

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.

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RNA Multiple Sequence Alignment


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Language:Perl 65.1%Language:C++ 33.0%Language:Shell 1.2%Language:Makefile 0.7%