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:
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- nucleotide sensitivity (Sn)
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- nucleotide specificity (Sp)
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- approximate correlation (AC)
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- correlation coefficient (CC)
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- exon sensitivity (ESn)
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- exon specificity (ESp)
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- proportion of real exons correctly predicted (CRa)
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- proportion of real exons partially predicted (PCa)
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- proportion of real exons with overlapping predictions (OLa)
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- missed exons (ME)
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- proportion of predicted exons that are correct (CRp)
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- proportion of predicted exons that are partially correct (PCp)
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- proportion of predicted exons that overlap real ones (OLp)
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- 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>
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(required) List of names of files defining real genes (GFF).
-p <pred_fname_list>
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(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
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certain nucleotide-level statistics.
-f <feat_list>
- List of names of all features denoting exon regions.
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By
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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.