Given multiple sequences with its secondary structures, produces a graphical representation of secondary structures conservation comparation with respect to one of the sequences. Expects directory containing fasta files (.fst) which includes (predicted) secondary structure and a list file, that contains names of the sequences that should be compared. First sequence in the list is always the primary, meaning all other sequences are compared to it.

Requires the following to be installed:

• Python (tested with version 2.7)
• RNAPlot, which can be downloaded as a part of the Vienna RNA package
• clustalw2, which can be found somewhat unorthodoxly at the Help page of its website

The compare.py script can be used as a standalone command-line tool.

Command-line usage

Run:

python compare.py --help

to get a description of all command-line parameters.

python compare.py bacteria

to run annotation on the included bacteria data.