1 / 10

The genome

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 welch@ohio.edu. genes. junk. The genome.

talon-porter
Télécharger la présentation

The genome

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. The WordSeeker Functional Genomics ToolkitLonnie Welch, Stuckey ProfessorBioinformatics LaboratoryElectrical Engineering and Computer Science Biomedical Engineering ProgramMolecular and Cellular Biology Program Ohio Universitywelch@ohio.edu

  2. genes junk The genome Genes: 3% Junk: 97% "So much junk DNA in our genome." (S. Ohno, 1972) "DNA differs from written language in that islands of sense are separated by a sea of nonsense, never transcribed." (Richard Dawkins, 2004)

  3. “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).

  4. “Perhaps it is time tobid 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) The genome genes Functional elements? Functional Elements: 90%?? Junk: 10%?? "...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)

  5. WordSeeker

  6. 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

  7. 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.

  8. 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)

  9. 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.

More Related