Methodology article

Quantitative measures for the management and comparison of annotated genomes

Karen Eilbeck, Barry Moore, Carson Holt and Mark Yandell^*

• * Corresponding author: Mark Yandell myandell@genetics.utah.edu

Author Affiliations

Department of Human genetics, Eccles Institute of Human Genetics, University of Utah and School of Medicine, Salt Lake City, Utah, USA

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BMC Bioinformatics 2009, 10:67 doi:10.1186/1471-2105-10-67

Published: 23 February 2009

Abstract

Background

The ever-increasing number of sequenced and annotated genomes has made management of their annotations a significant undertaking, especially for large eukaryotic genomes containing many thousands of genes. Typically, changes in gene and transcript numbers are used to summarize changes from release to release, but these measures say nothing about changes to individual annotations, nor do they provide any means to identify annotations in need of manual review.

Results

In response, we have developed a suite of quantitative measures to better characterize changes to a genome's annotations between releases, and to prioritize problematic annotations for manual review. We have applied these measures to the annotations of five eukaryotic genomes over multiple releases – H. sapiens, M. musculus, D. melanogaster, A. gambiae, and C. elegans.

Conclusion

Our results provide the first detailed, historical overview of how these genomes' annotations have changed over the years, and demonstrate the usefulness of these measures for genome annotation management.