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DOE JGI produces new QC tool for microbial genomes
Date:5/25/2010

ardized output, thus not only significantly improving quality, but also significantly facilitating comparative analysis."

Dawn Field, President of the Genomics Standards Consortium, an international initiative of genomics researchers interested in establishing standards for collecting and capturing genomic data to the general community, called GenePRIMP "a great solution to a long-standing problem in computational bioinformatics - how to clean up gene calls based on comparative genomic data. Ideally," she added, "the underlying principles will pave the way for new standards in gene calling."

GenePRIMP is available for use by researchers at http://geneprimp.jgi-psf.org/. Genomics researchers supported by a range of federal agencies and other funding sources are expected to take advantage of this new quality control tool. The current version of the software finds and reports gene model anomalies to the scientists. Pati said that a future version of GenePRIMP will automatically find and correct said anomalies as well as report frameshifts (genetic mutation caused by insertion or deletion of nucleotides) and pseudogenes.

"Consistent high-quality annotation on microbial genomes is key to their utility," said Owen White, director of bioinformatics at the University of Maryland School of Medicine and head of the Human Microbiome Project Data Analysis and Coordination Center that tracks, stores, analyzes and distributes the data. "Software such as GenePRIMP is an important component in our quality control toolbox."

Pati said the automated software tool is the crystallization of manual operating procedures used for more than 3 years for correcting gene models at the DOE JGI. "As such, it is also following the principles of standardization of the Genomics Standards Consortium and further development will factor in the Consortium's recommendations," she and her colleagues wrote, while enabling f
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Contact: David Gilbert
degilbert@lbl.gov
925-296-5643
DOE/Joint Genome Institute
Source:Eurekalert  

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