Upload
talon-porter
View
42
Download
0
Tags:
Embed Size (px)
DESCRIPTION
The WordSeeker Functional Genomics Toolkit Lonnie Welch, Stuckey Professor Bioinformatics Laboratory Electrical Engineering and Computer Science Biomedical Engineering Program Molecular and Cellular Biology Program Ohio University [email protected]. genes. junk. The genome. - PowerPoint PPT Presentation
Citation preview
The WordSeeker Functional Genomics Toolkit
Lonnie Welch, Stuckey ProfessorBioinformatics Laboratory
Electrical Engineering and Computer Science Biomedical Engineering Program
Molecular and Cellular Biology Program Ohio University [email protected]
The genome
genes
junk
Genes: 3% Junk: 97%
"DNA differs from written language in that islands of sense are separated by a sea of nonsense, never transcribed." (Richard Dawkins, 2004)
"So much junk DNA in our genome." (S. Ohno, 1972)
“The aim of the ENCODE (encyclopaedia of DNA elements) project is to identify every sequence with functional properties in the human genome.
Some highlights of the pilot phase of this project:
•involved an analysis of 1% (30 megabases) of the human genome
•remarkably:•much functional information is not “conserved” across organisms
•up to 93% of bases in the ENCODE regions are transcribed
•not good news for genes, which will no longer be able to hog the limelight
•the genome is much more than a mere vehicle for genes
[1] John M. Greally, Genomics: Encyclopaedia of humble DNA, Nature 447, 782-783 (14 June 2007).
The genome genes
Functional elements?
Functional Elements: 90%?? Junk: 10%??
“Perhaps it is time to bid farewell to the term ‘junk’ DNA – we knew not your true nature.” (Regulatory RNAs and the demise of ‘junk’ DNA. Genome Biology 2006, 7:328)
"...a certain amount of hubris was required for anyone to call any part of the genome 'junk, ' given our level of ignorance."(Francis Collins, 2006)
WordSeeker
WordSeeker Users
OU• Sarah Wyatt (NSF, NASA) – plant gravitropism; regulatory genomics• Allan Showalter (NSF, USDA) – cell wall genes; functional genomics• Susan Evans (NIH) – regulatory aspects of cancer
OARDC• Eric Stockinger (NSF) – cold tolerance in crops
OSU• Erich Grotewold (NSF, USDA, DOE) – genome-wide regulatory genomics• Rebecca Lamb (NSF) – cell development
BGSU• Paul Morris (NSF, DOE) – homology in Oomycete promoters
National Human Genome Research institute (NIH)• Laura Elnitski – regulatory aspects of cancer
Centers for Disease Control• Henry Wan – avian flu
Genome Database
• organized in six major organism groups: Archaea, Bacteria, Eukaryotae, Viruses, Viroids, and Plasmids
• provides views for a variety of genomes, complete chromosomes, sequence maps with contigs, and integrated genetic and physical maps
source: National Center for Biotechnology Information, April 2008.
Additional Suggestions(Prof. Frank Drews, OU EECS)
Desirable hardware features: Memory intense applications utilizing many cores will
saturate the front-side busses Large number of cores high front-side bus bandwidth
Large last-level caches Equip cluster nodes with the new Graphics Processing
Units (GPU’s) (such as NVIDIA's GeForce 8800 series GPU's) for memory intense algorithms Can off-load some processing to these GPU’s A number of recent bioinformatics algorithms run on
these GPU’s and show impressive speed-ups • E.g., M. Schatz, C. Trapnell, A. Delcher, A. Varshney,
High-throughput sequence alignment using Graphics Processing Units, BMC Bioinformatics, Vol. 8, No. 1. (2007)
Ohio Bioinformatics Consortium Statewide Bioinformatics Curriculum
Comprehensive curriculum Shared courses Managed by Ralph Regula School
Bioinformatics Research Infrastructure State-of-the-art Biological researchers define requirements Bioinformatics researchers design algorithms to meet
requirements Ohio Supercomputer Center integrates, hosts and supports
bioinformatics software
$9M will be invested over the next 5 years via Choose Ohio First.