Navigation Links
California computer scientists double volume of data in NIH biotech repository

nucleotide polymorphisms (SNPs), which are sites in the DNA sequence where individuals differ at the level of nucleotides.

These SNPs (pronounced snips) are locations in the human DNA sequence where two possible bases occur in the population. SNPs account for the most common type of variation in DNA sequence in humans and due to the recently developed high-throughput genotyping technology, genotype information on an individual's SNPs can be collected very cheaply.

Enter computational biologists around the world who have been devising ways to infer or extrapolate these haplotypes from the flood of genotype data produced by DNA sequencing efforts. Eskin and Ph.D. candidates Noah Zaitlen and Hyun Min Kang at UCSD, and research scientist Eran Halperin at ICSI, worked with NCBI scientists Michael Feolo and Stephen Sherry to infer haplotypes based on all of the data from genotyping studies deposited in NCBI's dbSNP database. Rather than use standard methods for inferring haplotypes, the computer scientists used HAP, a software tool originally developed at ICSI by Halperin and Richard Karp in collaboration with Eskin.

They ran the HAP algorithm on all dbSNP data sets using a cluster of 30 Intel Xeon processors provided by Calit2's National Science Foundation-funded OptIPuter project, in cooperation with the National Biomedical Computation Resource. Both organizations are based at UCSD. "In under 24 hours we were able to process more than 286 million haplotypes, partition those haplotypes into blocks, or regions, of limited diversity, and determine a set of 'tag' SNPs that capture the majority of genetic variation," explained Halperin.

The researchers' article appears in a special issue of Genome Research on "Human Genetic Variation," and its publication coincides with the release of a wide-ranging genotype study by the International HapMap Consortium in the journal Nature. The group's HapMap is a map of haplotype blocks and the ta
'"/>

Source:University of California - San Diego


Page: 1 2 3 4

Related biology news :

1. Scientists discover unique microbe in Californias largest lake
2. New Species of Coral Discovered Off Southern California
3. Seal rookeries could provide a reliable food source for endangered California condors, study finds
4. UCR environmental scientists propose chemical solution to cleaning Californias Salton Sea
5. Researchers develop flood-tolerant California rice
6. Supercomputer Dedicated To Bioengineering, Computational Biology Installed
7. Programmable cells: Engineer turns bacteria into living computers
8. Supercomputers to focus brains on AIDS dilemma
9. Designing vaccines by computer
10. Using computers and DNA to count bacteria
11. UNC computer, marine scientists collaborate to predict flow of toxic waters from Katrina
Post Your Comments:
(Date:11/21/2014)... DALLAS , November 18, 2014 ... Security Systems Market by Systems (Video, RFID, Access Control, ... (SEZ, Factories, Hotels, Banks, Government), Component Service Geography - ... Security Systems Market is projected to be around $25 ... Billion by 2020, growing at a CAGR of 8.69%. ...
(Date:11/21/2014)... NEW YORK , Nov. 19, 2014  Earlier ... Board at New York College, and one of the ... for biosensor signals that are transmitted from Smartphones to ... there were Smartphones and has one of the earliest ... are discussing its usage in the military, child care, ...
(Date:11/21/2014)... 2014 Strict laws against distracted driving and ... North American and European automotive sector towards gesture recognition ... systems that are intuitive and able to retrieve information ... New analysis from Frost & Sullivan,s ... Europe and North ...
Breaking Biology News(10 mins):Industrial Security Systems Market Worth $38 Billion by 2020 2Industrial Security Systems Market Worth $38 Billion by 2020 3Patented Biosensor Wearable Technology Provides a More Civilized Method of Quarantine 2Patented Biosensor Wearable Technology Provides a More Civilized Method of Quarantine 3Patented Biosensor Wearable Technology Provides a More Civilized Method of Quarantine 4Gesture Recognition Intensifies with the Rise of In-car Smartphone Integration, Says Frost & Sullivan 2Gesture Recognition Intensifies with the Rise of In-car Smartphone Integration, Says Frost & Sullivan 3Gesture Recognition Intensifies with the Rise of In-car Smartphone Integration, Says Frost & Sullivan 4
... medical woes ranging from cancer to bird flu will ... The newly-patented device will offer small and medium-sized researchers ... It will also allow them a chance, at last, ... analyze drugs and view the characteristics of protein. ...
... a gene known to increase the risk of Alzheimer,s ... Oregon Health & Science University study has found. ... that 7- to 10-year-olds with a member of a ... and neuroprotection display reduced spatial learning and memory, associated ...
... include: continental deformation and the San Andreas fault; ... between Britain and America; environmental stress and the ... Canada,s Mackenzie River basin as a CO2 source ... the absence of active volcanism; and geologic evolution ...
Cached Biology News:Council to honor NJIT SmartPin 2Children with gene show reduced cognitive function 2November GEOLOGY and GSA TODAY Media Highlights 2November GEOLOGY and GSA TODAY Media Highlights 3November GEOLOGY and GSA TODAY Media Highlights 4November GEOLOGY and GSA TODAY Media Highlights 5November GEOLOGY and GSA TODAY Media Highlights 6November GEOLOGY and GSA TODAY Media Highlights 7November GEOLOGY and GSA TODAY Media Highlights 8November GEOLOGY and GSA TODAY Media Highlights 9November GEOLOGY and GSA TODAY Media Highlights 10
(Date:11/26/2014)... The ETC (Emerging Technology Centers) http://www.etcbaltimore.com , ... that applications for AccelerateBaltimore™ (AB) 2015 program will ... a big idea?,” asked ETC’s President Deb Tillett. ... AccelerateBaltimore helps you and your big idea go ... Interested game changers with “big ideas” should ...
(Date:11/26/2014)... November 25, 2014 Silicon Valley Electronic ... with RPM Alliance , provider of clinical research ... With the latest addition to its CRO Partnership Program, ... EDC system to India. , “We have found ... and customizable EDC platform which is both user friendly ...
(Date:11/26/2014)... 25, 2014 Miles Holder, formerly of ... Graphel Carbon Products team as Sales/Marketing Manager. Mr. Holder ... customer service for the graphite industry. , “We are ... team,” stated Dave Trinkley, VP of Market and Product ... of experience in the graphite industry, along with his ...
(Date:11/26/2014)... 2014 Theravalues Corporation est fier d,annoncer ... européen au salon Hi Europe 2014 (du 2 ... Curcumine la plus biodisponible actuellement sur ... à des ingrédients approuvés par les règlements européens. ... présent dans la racine de curcuma ( Curcuma ...
Breaking Biology Technology:AccelerateBaltimore Applications to Close in 6 Days 2AccelerateBaltimore Applications to Close in 6 Days 3RPM Alliance Joins Clinovo’s CRO Partnership Program, Further Strengthening Its Presence in Southern California and India 2Miles Holder Joins Graphel Corporation as Sales/Marketing Manager 2La curcumine présentant la plus haute biodisponibilité bientôt en vente en Europe 2La curcumine présentant la plus haute biodisponibilité bientôt en vente en Europe 3
... required regulatory approvals for the $2.3 billion acquisition of ... divest of two divisions of the company they are ... manufacturer plans to integrate Instrumentarium it into its ... CEO, Dow Wilson.. , ,The final required ...
... to open a new state-of-art healthcare facility in October, ... latest in digital imaging technology from technology vendor Emageon. ... and distribution of digital medical images across its integrated ... in 1984 is a nationally recognized leader in efforts ...
... Internet connection? , ,MADISON, WI - McDonalds ... connections in five Milwaukee locations as part of a ... restaurants in the San Francisco Bay Area, Metropolitan New ... McDonald's Wireless Internet service. , ,Customers can purchase an ...
Cached Biology Technology:Aurora Selects New Imaging Technology 2Wisconsin McDonalds Go Wireless 2
... Edition of Molecular Imaging (MI) Software for ... science research and drug discovery applications. The ... Food and Drug Administrations Code of Federal ... Electronic Signatures [21 CFR Part 11]. KODAK ...
... Tissue Arrays are intended for laboratory research ... fixed in neutral buffered formalin and embedded ... was performed by certified pathologists. Tissue ... and relocated into a new recipient paraffin ...
... industry standard microarray image analysis software because ... analysis tools, visualizations, automation capabilities, performance and ... with every GenePix scanner, and it also ... all types of arrays. A wide range ...
... applications not requiring confocal, the BD Pathway ... the Pathway 435. And, the Pathway 415 ... applications require it. High-performance, ... to use the laser autofocus, camera autofocus, ...
Biology Products: