Navigation Links
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
'/>"/>

Contact: David Gilbert
degilbert@lbl.gov
925-296-5643
DOE/Joint Genome Institute
Source:Eurekalert  

Page: 1 2 3 4

Related biology news :

1. Plasma produces KO cocktail for MRSA
2. Iowa State researcher produces, ships only H1N1 vaccine available for swine
3. Switchgrass produces biomass efficiently
4. Accidental discovery produces durable new blue pigment for multiple applications
5. UC Davis challenge produces a better air conditioner
6. Wastewater produces electricity and desalinates water
7. Researchers describe implausible chemistry that produces herbicidal compound
8. Obscure fungus produces diesel fuel components
9. Ethanol byproduct produces green results
10. New chemotherapy combo produces side effects, but no extra efficacy, in early breast cancer patients
11. New study shows Dermytol produces pronounced decrease in malignant melanoma tumor volume
Post Your Comments:
*Name:
*Comment:
*Email:
Related Image:
DOE JGI produces new QC tool for microbial genomes
(Date:7/11/2014)... of mesenchymal stem cells can stimulate neurogenesis in the ... disease (AD) and improve tissue and function injury under ... on the therapeutic effect of adipose-derived stem cells (ADSCs) ... on oxidative injury and neurogenesis in the brain of ... of Life Sciences, Tsinghua University, China transplanted ADSCs into ...
(Date:7/11/2014)... that cannabinoid receptor type 1 can inhibit ... and reduce neurotransmitter release. However, some scholars ... increase extracellular Ca2+ influx and increase neurotransmitter ... Tongji Hospital Affiliated to Tongji Medical College, ... used whole cell voltage-clamp and calcium imaging ...
(Date:7/11/2014)... of all vertebrates, information is transmitted through synapses, ... signal to be passed from one brain cell ... abundant type of synapse, can be either excitatory ... memory, perception and cognition, and the balance between ... For instance, every time we learn something, ...
Breaking Biology News(10 mins):Blame it on the astrocytes 2
... a study in her lab showed that mate (mah ... the activity of an enzyme that promotes HDL (good) ... scientist Elvira de Mejia headed for Argentina where mate ... She returned with a five-year agreement signed by ...
... rare Amur leopard (Panthera pardus orientalis), one of only ... captured and health-checked by experts from a consortium of ... group of organizations, including the Russian Academy of Sciences ... (WCS) and the Zoological Society of London (ZSL) captured ...
... more than 50 Earth Observation satellites is increasing ... synoptic views of our planet. Because these satellites ... analysis and environmental monitoring can be difficult, making ... Calibration and Validation processes. More than 50 ...
Cached Biology News:More on mate tea: lower cholesterol and an international agreement 2Critically endangered Amur leopard captured 2A roadmap for calibration and validation 2
(Date:7/13/2014)... 2014 Deep Research Report on Global and ... study on the current state of the Nano Silver ... a basic overview of the industry, including definitions, applications ... domestic market analysis are provided with a focus on ... A comparison between the international and Chinese situation is ...
(Date:7/11/2014)... WEST PALM BEACH, Fla. , July 11, 2014 ... wide variety of high-quality peptides that are used solely ... online. To honor two successful years in business, Maxim ... Performance LLC, has just launched a new and updated ... addition, the research blog section has been updated with ...
(Date:7/11/2014)... DUBLIN , July 11, 2014 ... "International Transfection Technology Market - Global Industry Analysis, ... report to their offering. ... to introduce nucleic acids (either DNA or RNA) into ... therapy, mutation of cancer cells and protein metabolism by ...
(Date:7/11/2014)... 2014 EPFL and the University of  ... of John P. Donoghue . The American neuroscientist ... . The new Wyss Center for ... Geneva , has named as its director ... P. Donoghue , founder of Brown University,s Institute for ...
Breaking Biology Technology:2014 Nano Silver Industry in Global and China Regions Development Proposals Analysis Available at DeepResearchReports.com 22014 Nano Silver Industry in Global and China Regions Development Proposals Analysis Available at DeepResearchReports.com 3Maxim Peptide Celebrates Second Anniversary Online with an Updated Website and Special Deals Section 2International Transfection Technology Market - Industry Analysis, Size, Share, Growth, Trends and Forecast to 2019 2John P. Donoghue is Taking the Lead at the Wyss Center and is Appointed Professor at EPFL and University of Geneva 2John P. Donoghue is Taking the Lead at the Wyss Center and is Appointed Professor at EPFL and University of Geneva 3
... 32 social scientists and researchers from around the world, ... have concluded that fundamental reforms of global environmental governance ... system. The scientists argued in the March 16 edition ... is now for a "constitutional moment" in world politics. ...
... 2012   Lexicon Pharmaceuticals, Inc. (Nasdaq: ... and Drug Administration (FDA) has granted its request for ... for the treatment of carcinoid syndrome.  Carcinoid syndrome is ... originate from the gastrointestinal tract and is characterized by ...
... 2012 AlphaVax, Inc. ("AVX") is pleased to report that it ... Industry Excellence Award as the Best Early-Stage Vaccine Biotech Company. The ... Washington, DC in April. AVX is pleased to ... the panel of judges as well as being recognized as a ...
Cached Biology Technology:Fundamental steps needed now in global redesign of Earth system governance 2Fundamental steps needed now in global redesign of Earth system governance 3FDA Grants Lexicon Orphan Drug Designation for Telotristat Etiprate for the Treatment of Carcinoid Syndrome 2FDA Grants Lexicon Orphan Drug Designation for Telotristat Etiprate for the Treatment of Carcinoid Syndrome 3FDA Grants Lexicon Orphan Drug Designation for Telotristat Etiprate for the Treatment of Carcinoid Syndrome 4
... The Rice Oligo Microarray, 22K ... of rice genes associated with biological ... abiotic stress response. Each microarray contains ... of the rice (japonica) genome focuses ...
... ELF 97 Cytological Labeling Kit provides a ... detection of cellular targets, including cell-surface receptors ... Labeling Kit contains the patented ELF 97 ... yellow-green precipitate at the site of enzymatic ...
... Ligands\n\nReceptor-related research has long been enabled by ... selected to keep pace with new discoveries. ... and services for receptor research and drug ... you do not find exactly what you ...
... Feature Extraction Software reads ... files to prepare microarray data ... , * one 2-year ... for NFP/Academic accounts , * ...
Biology Products: