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Table 1 Annotation comparison methods

From: ParsEval: parallel comparison and analysis of gene structure annotations

Method

Pros

Cons

Manual comparison

minimal overhead

extremely tedious; error prone; unscalable

Genome browser

intuitive interface; visual assessment of individual loci

visual assessments imprecise; extensive overhead; little or no automation

Eval

detailed statistics; visual assessment of statistic distributions; scales fairly well for large data sets; can compare multiple predictions to a single reference

older software; relatively slow; only summary statistics are reported, while stats for individual loci are discarded

ParsEval

detailed statistics provided, not only as a summary but for individual loci as well; scales well for large data sets; fast, efficient, and portable

only capable of comparing a single pair of annotations

  1. Various approaches to comparing alternative sources of gene structure annotations, with a brief description of the associated pros and cons.