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

. For example, genes acquired by horizontal gene transfer could become pseudogenes (similar to genes but not coding for a gene product) and are more error-prone. Pati said GenePRIMP significantly reduces the amount of time scientists spend checking the whole genome by specifically highlighting errors that need to be manually corrected.

"Without a GenePRIMP report to work with," she said, singling out the microbe Starkeya novellaa soil bacterium that plays an important role in regulating the cycling of carbon and sulfuras an example, "a DOE JGI scientist would have to examine 4,480 gene models. With GenePRIMP they have to examine less than a tenth of that number of genes." She said that the GenePRIMP report offers additional value because it already includes any anomalies found through BLAST (Basic Local Alignment Search Tool), which finds regions of local similarity between sequences, so scientists don't have to run their own BLAST search.

"With GenePRIMP we have achieved a major breakthrough in the improvement of the quality of structural annotations such as gene predictions," said Genome Biology Program head and study senior author Nikos Kyrpides. He pointed out that using GenePRIMP offers researchers three major advantages: high quality results with reduced errors; an approach that can be used regardless of the automated software originally used to check gene annotations; and finally a method to standardize gene calling.

"There are a lot of different tools used for predicting genes in prokaryotes," Kyrpides said. "The major problem we have is that they all produce very variable results. This impedes our ability to compare genomes sequenced and annotated from various sources, as they use different tools for gene prediction. GenePRIMP is not substituting any of the available methods; a user can employ any available automatic gene prediction method, and then use GenePRIMP to correct the initial output. It will generate a much more stand
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Contact: David Gilbert
degilbert@lbl.gov
925-296-5643
DOE/Joint Genome Institute
Source:Eurekalert  

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