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Bioinformatics Advance Access originally published online on June 27, 2009
Bioinformatics 2009 25(17):2271-2278; doi:10.1093/bioinformatics/btp393
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

IMG ER: a system for microbial genome annotation expert review and curation

Victor M. Markowitz 1,*, Konstantinos Mavromatis 2, Natalia N. Ivanova 2, I-Min A. Chen 1, Ken Chu 1 and Nikos C. Kyrpides 2

1 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 and 2 Genome Biology Program, DOE Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, CA 94598, USA

* To whom correspondence should be addressed.


  Abstract

Motivation: A rapidly increasing number of microbial genomes are sequenced by organizations worldwide and are eventually included into various public genome data resources. The quality of the annotations depends largely on the original dataset providers, with erroneous or incomplete annotations often carried over into the public resources and difficult to correct.

Results: We have developed an Expert Review (ER) version of the Integrated Microbial Genomes (IMG) system, with the goal of supporting systematic and efficient revision of microbial genome annotations. IMG ER provides tools for the review and curation of annotations of both new and publicly available microbial genomes within IMG's rich integrated genome framework. New genome datasets are included into IMG ER prior to their public release either with their native annotations or with annotations generated by IMG ER's annotation pipeline. IMG ER tools allow addressing annotation problems detected with IMG's comparative analysis tools, such as genes missed by gene prediction pipelines or genes without an associated function. Over the past year, IMG ER was used for improving the annotations of about 150 microbial genomes.

Contact: vmmarkowitz{at}lbl.gov

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Alex Bateman

Received on April 15, 2009; revised on June 20, 2009; accepted on June 22, 2009

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Home page
 Nucleic Acids ResHome page
V. M. Markowitz, I-M. A. Chen, K. Palaniappan, K. Chu, E. Szeto, Y. Grechkin, A. Ratner, I. Anderson, A. Lykidis, K. Mavromatis, et al.
The integrated microbial genomes system: an expanding comparative analysis resource
Nucleic Acids Res., October 28, 2009; (2009) gkp887v1.
[Abstract] [Full Text] [PDF]


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