NAME

locarna_mcc

SYNOPSIS

locarna_mcc -f=<annotation_file> [options] aln_file(s)

Computes the MCC (Mathew's correlation coefficient) along with several other secondary structure prediction performance measures for structures predicted by RNAalifold from one or several alignments in CLUSTAL W format.

Options:

-f=<annotation_file>

    Structure annotation file. Mandatory argument.
    

-P=<param_file>

    Parameter file for RNAalifold
    

--alifold-args

    Alifold arguments (default: same as mlocarna)
    

--assume-fasta

    Assume that input is in fasta format (instead of clustalw aln)
    

--help

    Brief help message
    

--man

    Full documentation
    

-v, --verbose

    Verbose
    

-q, --quiet

    Quiet
    

DESCRIPTION

For each file produce an output line <name> <tp> <fp> <fn> <tn> <ppv> <sens> <mcc> <sqrt($sens*$ppv)>

The structure annotation file contains lines of <name> <sequence> <structure> and must contain an entry for each sequence in the alignment.