Quantitative measures for the management and comparison of annotated genomes.
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.


CONCLUSIONS
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.
Eilbeck
Karen
K
Department of Human genetics, Eccles Institute of Human Genetics, University of Utah and School of Medicine, Salt Lake City, UT, USA. keilbeck@genetics.utah.edu
Moore
Barry
B
Holt
Carson
C
Yandell
Mark
M
D017398:Alternative Splicing; D000818:Animals; D030541:Databases, Genetic; D016678:Genome; D023281:Genomics / Q000379:methods*