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dc.contributor.author Standage, D.S. en
dc.contributor.author Brendel, V.P. en
dc.date.accessioned 2014-11-04T13:17:32Z en
dc.date.available 2014-11-04T13:17:32Z en
dc.date.issued 2012 en
dc.identifier.citation Standage, D. S., & Brendel, V. P. (2012). ParsEval: Parallel comparison and analysis of gene structure annotations. BMC Bioinformatics, 13, 187. http://dx.doi.org/10.1186/1471-2105-13-187 en
dc.identifier.uri http://hdl.handle.net/2022/19113
dc.description.abstract 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 http://parseval.sourceforge.net/. en
dc.language.iso en_US en
dc.publisher BioMed Central Ltd. en
dc.relation.isversionof https://doi.org/10.1186/1471-2105-13-187 en
dc.rights © 2012 Standage and Brendel. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. en
dc.rights.uri http://creativecommons.org/licenses/by/2.0 en
dc.subject Biological insight en
dc.subject End-users en
dc.subject Eukaryotic genome en
dc.subject Gene model en
dc.subject Gene prediction en
dc.subject Gene structure en
dc.subject Genome annotation en
dc.subject Genome browsers en
dc.subject Genome projects en
dc.subject Genomic locus en
dc.subject Memory consumption en
dc.subject Pair-wise comparison en
dc.subject Parallel comparisons en
dc.subject Performance improvements en
dc.subject Runtimes en
dc.subject Software applications en
dc.subject Software developer en
dc.subject Source codes en
dc.subject Systematic identification en
dc.subject Work-flows en
dc.subject Application programs en
dc.subject Laptop computers en
dc.subject Genes en
dc.subject Eukaryota en
dc.subject article en
dc.subject biology en
dc.subject computer program en
dc.subject genetic database en
dc.subject genomics en
dc.subject human en
dc.subject methodology en
dc.subject molecular genetics en
dc.subject Computational Biology en
dc.subject Databases, Genetic en
dc.subject Molecular Sequence Annotation en
dc.subject Software en
dc.title ParsEval: Parallel comparison and analysis of gene structure annotations en
dc.type Article en
dc.altmetrics.display true en


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