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:7/22/2014)... of Standards and Technology (NIST), working with the ... for analyzing biological cells and tissues based on ... is an advanced form of the widely used ... that are 10,000 times stronger than obtained from ... obtained from comparable "coherent Raman" instruments, and uses ...
(Date:7/22/2014)... as disease causing agents, some viruses can perform ... shape the world we live in today, according ... of Microbiology. , "Viruses participate in essential Earth ... planet, from contributing to biogeochemical cycles, shaping the ... Marilyn Roossinck of Pennsylvania State University, a member ...
(Date:7/22/2014)... Stem cells offer much promise for treating damaged organs ... survival is poor, limiting their effectiveness. New methods are ... optimize their therapeutic function after transplantation, as described in ... a peer-reviewed journal from Mary Ann Liebert, Inc., publishers. ... Open Access website . , In ...
Breaking Biology News(10 mins):Enhanced NIST instrument enables high-speed chemical imaging of tissues 2Enhanced NIST instrument enables high-speed chemical imaging of tissues 3Report on viruses looks beyond disease 2
... key to the blinding effects of diabetic retinopathy is ... Georgia researchers said. Interleukin-6, known to contribute ... helps ignite inflammation of the retina, a first step ... blindness is working-age adults, MCG researchers reported online in ...
... of dollars each year on exotic smelling perfumes and lotions ... a new study in Psychological Science , a journal ... be the best way to capture a potential mate,s attention. ... habits: Animal studies have shown that male testosterone levels are ...
... Malaga have created the ,Inventory of Daily Stressors, a ... physical appearance, taking part in numerous extracurricular activities and ... that increase the risk of suffering from childhood stress. ... to assess daily stress amongst schoolchildren", Mara Victoria Trianes, ...
Cached Biology News:Discovery points toward anti-inflammation treatment for blinding disease 2A new method to measure childhood stress 2
(Date:7/22/2014)... , July 22, 2014 Hussey Copper ... MD-Cu 29 antimicrobial copper announces Pullman Regional Hospital,s ... first EPA-registered antimicrobial solid touch surface, at a nominal ... of MRSA, E-coli and other bacteria within 2 hours of ... protecting against bacteria and infectious diseases in its facilities. ...
(Date:7/22/2014)... Md. , July 22, 2014  United ... today that it will release its second quarter ... July 29, 2014. United Therapeutics will ... 2014, at 9:00 a.m. Eastern Time.  The teleconference ... dialing 1-970-315-0533.  A rebroadcast of the teleconference will ...
(Date:7/22/2014)... 2014 Dr. Williams says, “Bush has ... recognized that the greatest health care system in the ... needlessly deadly while trying to serve the public. Unfortunately, ... to transform an enormous system that none of them ... his continuing series of Open Letters ( http://is.gd/wdU2CM ) ...
(Date:7/21/2014)... The yield so far is small, but chemists ... solution-based mineral substitution process to make a precursor to ... and alternative energy devices. , A paper describing the ... 21 issue of the journal Inorganic Chemistry , ... inorganic and nuclear chemistry fields. The paper was chosen ...
Breaking Biology Technology:Pullman Regional Hospital changes more than 1,100 touch points to Hussey Copper's MD-Cu29 antimicrobial copper to help protect against bacteria 2Pullman Regional Hospital changes more than 1,100 touch points to Hussey Copper's MD-Cu29 antimicrobial copper to help protect against bacteria 3Dr. Ira Williams Asks What’s Wrong With Jonathan Bush’s Book, Where Does It Hurt? 2Oregon chemists eye improved thin films with metal substitution 2
... , SEATTLE, Aug. 5 ... Murray, M.D., Ph.D. as Vice President of Clinical Development. ... at Omeros, and currently is leading the ongoing clinical ... the Company,s lead candidate being evaluated in a Phase ...
... The FIME 2009 ... John Rizvi will deliver a presentation titled, "Preservation of Legal Rights in Medical Innovations" at ... ... 2009 at 1:00 PM, attorney John Rizvi will deliver a presentation titled, "Preservation of Legal ...
... to develop organic solar cells that can be produced easily ... to generate electricity. But a major obstacle is coaxing ... the nanoscale (tinier than 2-millionths of an inch) to be ... to develop cells made from low-cost plastics that will transform ...
Cached Biology Technology:Omeros Appoints New Vice President of Clinical Development 2Patent Attorney John Rizvi Speaks at FIME International Medical Expo 2Plastics that convert light to electricity could have a big impact 2Plastics that convert light to electricity could have a big impact 3