NAME

       eval_predictions - Compares predicted genes with "real" (or annotated) genes.

SYNOPSIS

       eval_predictions -r <real_fname_list> -p <pred_fname_list> -l <seq_len_list> [OPTIONS]

DESCRIPTION:

       Compares  predicted  genes with "real" (or annotated) genes.  Reports standard measures of
       prediction quality.  The following measures are reported:

              - nucleotide sensitivity (Sn)

              - nucleotide specificity (Sp)

              - approximate correlation (AC)

              - correlation coefficient (CC)

              - exon sensitivity (ESn)

              - exon specificity (ESp)

              - proportion of real exons correctly predicted (CRa)

              - proportion of real exons partially predicted (PCa)

              - proportion of real exons with overlapping predictions (OLa)

              - missed exons (ME)

              - proportion of predicted exons that are correct (CRp)

              - proportion of predicted exons that are partially correct (PCp)

              - proportion of predicted exons that overlap real ones (OLp)

              - wrong exons (WE)

       All quantities are computed as  described  in  "Evaluation  of  Gene-Finding  Programs  on
       Mammalian Sequences," by Rogic et al. (Genome Research 11:817-832).  Note that CRa + PCa +
       OLa + ME = 1 and CRp + PCp + OLp + WE = 1.  Note also that each set (predicted  and  real)
       should consist of non-overlapping groups of features (see 'refeature').

OPTIONS

       -r <real_fname_list>

              (required) List of names of files defining real genes (GFF).

       -p <pred_fname_list>

              (required)  List of names of files defining predicted genes (GFF).  Must correspond
              in order to <real_fname_list>.

       -l <seq_len_list> (required) List of lengths of sequences.  Needed to compute

              certain nucleotide-level statistics.

       -f <feat_list>

       List of names of all features denoting exon regions.
              By

              default, equal to the single name "CDS".

       -d <fname_prefix> Dump full coords of  correct,  partially  correct,  wrong,  missed,  and
              overlapping exons to a set of files having the specified file name prefix.

       -n  <nbases>  Also  report stats on "nearly correct" exons, that is, incorrect exons whose
              boundaries are within <nbases> of being correct.  Columns will be labeled "NCa" and
              "NCp".

       -h Print this help message.

       NOTE:  be sure stop codons are included in CDSs in both the predicted and real sets, or in
       neither set.