Journal Article

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

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

in Bioinformatics

Volume 25, issue 17, pages 2271-2278
Published in print September 2009 | ISSN: 1367-4803
Published online June 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp393
IMG ER: a system for microbial genome annotation expert review and curation

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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@lbl.gov

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  5540 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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