Chess2FLYA 1.1  (05.04.2015)
--------------


NAME

    chess2flya -- Chemical shift prediction for RNA


SYNOPSIS

    chess2flya [-h] [-c num] [-f statistics-file] [-s sequence-file] [-w macro-file]


DESCRIPTION

    The program Chess2FLYA uses as input a file with RNA sequence and secondary structure
    information in the .ct file format. This can be created manually or e.g. on www.rnasoft.ca.
    Chess2FLYA uses chemical shift statistics (statfile.tab) that were evaluated considering the
    neighbouring nucleotides and their position in the secondary structure (loop, bulge, stem,
    mismatch,....). Using these input data, Chess2FLYA generates a file (cyana.prot) containing 
    predicted chemical shifts of all nucleotides of RNAs. Additionally an angle restraint file 
    (cyana.aco) and a sequence file (cyana.seq) are prepared. These files can be used for 
    automated assignment with the FLYA algorithm within CYANA. 

    The following options are available:

    -h	help
    -c	prediction interval defined by the percentage of resonances in it [1-11] (default: 2)
        1: 50%, 2: 60%, 3: 70%, 4: 80%, 5: 90%, 6: 95%, 7: 98%, 8: 99%, 9: 99.5%, 10: 99.8%, 11: 99.9%
    -f	input file with statistics table (default statfile.tab)
    -s	input file with RNA sequence and secondary structure (default: rna.ct)
	The file has to be in .ct format and can be created e.g. on http://www.rnasoft.ca/.
    -w	output CYANA macro to generate Watson-Crick H-bond restraints (default: none)


FILES

    chess2flya         script to start Chess2FLYA
    chess2flya.Linux   executable for Linux, called by Chess2FLYA
    chess2flya.Darwin  executable for Mac, called by Chess2FLYA
    statfile.tab       RNA chemical shift statistics table

    FZL4.ct	       example file with RNA sequence and secondary structure;
    		       can be created e.g. on http://www.rnasoft.ca/

    rnaflya.cya        example CYANA macro to run Chess2FLYA and FLYA automated assignment
    rna.lib	       additional CYANA library with rules for expected NOESY peaks
    *.peaks	       example input peak lists for FLYA


EXAMPLES

    Run Chess2FLYA alone: 
    
        ./chess2flya -s FZL4.ct -w wc.cya
    
    Run Chess2FLYA and FLYA: 
    
        cyana rnaflya


REFERENCE

    When reporting results obtained with Chess2FLYA, please cite this publication:

    Aeschbacher, T., Schmidt, E., Blatter, M., Maris, C., Duss, O., Allain, F. H.-T.,
    Guentert, P. & Schubert, M. Automated and assisted RNA resonance assignment using
    NMR chemical shift statistics. Nucl. Acids Res. 41, e172 (2013)
    

BUGS

    On some computers it is necessary to increase the stacksize with the Unix command:
    limit stacksize unlimited
    
    The input file with chemical shift statistics must not exceed 20000 lines. Other
    input files must not exceed 10000 lines.

