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MARNA

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MARNA


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You can try to run MARNA on your local machine. I have written a preliminary version which is executable on my machine and hopefully on your machine as well. I use a 2.8 GHz Pentium IV machine, kernel version 2.6. OS: Suse Linux 9.2. If you have a similar machine and if you have installed T-Coffee, the RNA Vienna Package, and RNAshapes then the chances are great that MARNA runs fully on your local machine.

  1. Install T-Coffee such that it can be run globally from any directory.
  2. Install Vienna RNA package (RNAfold/RNAsubopt) and/or RNAshapes such that it can be run globally from any directory.
  3. Download MARNA-100729.tar.gz.
  4. Unpack it with tar -xzf MARNA-100729.tar.gz.
  5. Change the unpacked source directory with cd MARNA.
  6. Check install notes and further information in file INSTALL.readme (e.g., with less INSTALL.readme).
  7. Compile with make.

Then test it with ./marna.pl test.efasta.

Reports are welcome!

If something seems to be wrong, then don’t hesitate to write an email to: rna[ @ ]informatik.uni-freiburg.de

Please cite:

Sven Siebert and Rolf Backofen, “MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons”, Bioinformatics 2005, Volume 21, Issue 16, 3352-3359 doi:10.1093/bioinformatics/bti550

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