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GenePRIMP QC tool on Genetic Engineering & Biotechnology News

The program, said Pati, identifies gene-calling errors such as potentially incorrect gene start and end positions, large overlaps between genes, fragmented genes and missed genes. Gene-calling errors, noted Pati, can range from two percent to as much as 30 percent of the original genes identified in the genome and are dependent on many factors, such… [Read More]

GenePRIMP QC tool on PhysOrg

“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… [Read More]

GenePRIMP QC tool on redOrbit

“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… [Read More]

GenePRIMP QC tool on ScienceDaily

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.  Read more on ScienceDaily. [Read More]

GenePRIMP QC tool on Medical News Today

More than a thousand microbial genomes have been sequenced at various sequencing centers in the past 15 years to better understand their roles in tasks ranging from bioenergy to health to environmental cleanup.  Read more on Medical News Today. [Read More]

GenePRIMP QC tool on EurekAlert

To assist in checking the quality of the microbial genomic DNA sequences generated before they are submitted to the federally funded public archive GenBank, the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) has introduced a quality control tool known as the Gene Prediction IMprovement Pipeline or GenePRIMP. GenePRIMP is described in a paper… [Read More]

JGI CIO announcement on HPC Wire

The Director of the Joint Genome Institute (JGI), Eddy Rubin, has announced that Victor Markowitz will serve as the new Chief Informatics Officer and Associate Director at JGI effective May 17, 2010. Read more on HPC Wire. [Read More]

Frog genome project on ScienceNews

A new study, published April 30 in Science, lays out the genetic blueprint of the Western clawed frog, Xenopus tropicalis. A larger cousin of X. tropicalis, called Xenopus laevis, is a popular laboratory organism for studying development. But with a genome about half the size of X. laevis’, the Western clawed frog has easier DNA… [Read More]

JGI CIO announcement on GenomeWeb

Markowitz will continue to lead the Biological Data Management and Technology Center while serving as a member of JGI’s senior management team, with responsibilities that include advising Director Eddy Rubin on issues concerning JGI’s technology infrastructure, how it can best be used, and what new equipment will be needed in the future. Read more on… [Read More]

Poplar bacteria project on EurekAlert

In the current study — through genome sequencing performed at DOE’s Joint Genome Institute, manual genome annotation in collaboration with Brookhaven biologist Sebastien Monchy, and metabolic analyses performed at the University of South Carolina in collaboration with Brookhaven plant scientist Lee Newman — the scientists identified an extended set of genes that help Enterobacter (sp…. [Read More]