This version of carnac can be use to detect significant common
structures in RNA sequences. It uses random sequences (original
sequences shuffled) to build an empirical distribution of the free
energy. Then structures observed on original sequences are evaluated
with a z-score of the free energy against the empirical distribution.

Carnac is used to find a common RNA structures of unaligned RNA
sequences. It has been written by O.Perriquet and H.Touzet. If you are
looking more information about carnac, please have a look here

	    http://bioinfo.lifl.fr

Random sequences are built from the original sequences by the program
'shuffle-aln.pl' (written by S.Washietl). This program produces
shuffles from an alignement: as our sequences are unaligned, we use
clustalw to align them before the shuffling and unaligned them
after. For more information on this program, please have a look here

   	    http://www.tbi.univie.ac.at



Supported inputs
----------------

For now, carnac only supports simple- and multi-FASTA formatted
files. All sequences passed in arguments of the command line are
treated together.


Example
-------

Some examples are available in the examples.carnac directory.

To execute carnac on one of the sequences, simply type something like:

   carnac examples.carnac/telomerase.fasta

If you plan to use carnac as a batch program, the following option could help you:

   -o dir    while put every outputs to the directory 'dir'. If the
             directory does not exist, it is created.


Enjoy!

Arnaud FONTAINE (arnaud.fontaine@lifl.fr)