ParsEval: Parallel comparison and analysis of gene structure annotations

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BioMed Central Ltd.


Background: Accurate gene structure annotation is a fundamental but somewhat elusive goal of genome projects, as witnessed by the fact that (model) genomes typically undergo several cycles of re-annotation. In many cases, it is not only different versions of annotations that need to be compared but also different sources of annotation of the same genome, derived from distinct gene prediction workflows. Such comparisons are of interest to annotation providers, prediction software developers, and end-users, who all need to assess what is common and what is different among distinct annotation sources. We developed ParsEval, a software application for pairwise comparison of sets of gene structure annotations. ParsEval calculates several statistics that highlight the similarities and differences between the two sets of annotations provided. These statistics are presented in an aggregate summary report, with additional details provided as individual reports specific to non-overlapping, gene-model-centric genomic loci. Genome browser styled graphics embedded in these reports help visualize the genomic context of the annotations. Output from ParsEval is both easily read and parsed, enabling systematic identification of problematic gene models for subsequent focused analysis. Results: ParsEval is capable of analyzing annotations for large eukaryotic genomes on typical desktop or laptop hardware. In comparison to existing methods, ParsEval exhibits a considerable performance improvement, both in terms of runtime and memory consumption. Reports from ParsEval can provide relevant biological insights into the gene structure annotations being compared. Conclusions: Implemented in C, ParsEval provides the quickest and most feature-rich solution for genome annotation comparison to date. The source code is freely available (under an ISC license) at



Biological insight, End-users, Eukaryotic genome, Gene model, Gene prediction, Gene structure, Genome annotation, Genome browsers, Genome projects, Genomic locus, Memory consumption, Pair-wise comparison, Parallel comparisons, Performance improvements, Runtimes, Software applications, Software developer, Source codes, Systematic identification, Work-flows, Application programs, Laptop computers, Genes, Eukaryota, article, biology, computer program, genetic database, genomics, human, methodology, molecular genetics, Computational Biology, Databases, Genetic, Molecular Sequence Annotation, Software


Standage, D. S., & Brendel, V. P. (2012). ParsEval: Parallel comparison and analysis of gene structure annotations. BMC Bioinformatics, 13, 187.


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© 2012 Standage and Brendel. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.