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From:
Published online Aug 1, 2012. doi: 10.1186/1471-2105-13-187
Table 1
Annotation comparison methods
MethodProsCons   
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
   
ParsEvaldetailed statistics provided, not only as a summary but for individual loci as well; scales well for large data sets; fast, efficient, and portableonly capable of comparing a single pair of annotations   
Various approaches to comparing alternative sources of gene structure annotations, with a brief description of the associated pros and cons.
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