COURSE_NOTES.txt

This file is only of interest to you if you were forced to download 
this bundle of scripts because you're taking part in the 201x (x \in {2,3}) 
Structural Bioinformatics lecture series of the University of Potsdam.
For your assignment you only need the following three files (you can 
delete the other ones or make fun of the source code, whatever rocks 
your boat.) 

***FILES IMPORTANT FOR YOUR ASSIGNMENT***
1. mca2bracket2.py -- the script you will be using to do your assign-
ment
2. mdg_dt.py -- the definition of the motif detection graph data 
structure (used by 1.)
3. minilib.py -- a dictionary of modified bases derived from the
original {A,C,G,U}-alphabet of RNA sequences (used by 1.)

***USAGE OF mca2bracket2.py***
In order to draw a bracket-string from an MC-Annotate output file call 
the script as follows:

python mca2bracket2.py <MC-Annotate-file>

The script will then output a number of status messages and will terminate
with the output of two bracket strings 'Structure with knots' and 'Knotless'.
The 'Structure with knots'-string contains all cis Watson-Crick base pairs 
that are contained in the structure, whereas the 'Knotless'-string only contains 
the true secondary structure (as deduced from the base pair information by MC-
Annotate), i.e. a structure without any kind of crossing or touching interaction.