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.