L8 - Lab 7 - Bioinformatics

L8 - Lab 7 - Bioinformatics - Bioinformatics and NCBI Dr...

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Bioinformatics and NCBI Dr. Jacob Mayfield October 20th, 2008 We have been liberated from the tyranny of the life cycles of organisms, from their modes of reproduction. We can do genetics now on everything, anything. Giant redwoods, grapes and, most importantly, human beings. - Nobel Laureate Sydney Brenner on DNA sequence.
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Acknowledgements Meara Davies Jane O John Gahagan Atoosa Firouzian Sarah Mogri Nick Pleskaz Mark Andre Elizabeth Boydston Rachel Doran
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Goals Learn how to use computational biology tools View the wealth of information as an asset Reinforce the central dogma Understand more about human genetic disease
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What Are We Sequencing? Genes E xpressed S equence T ags (mRNA) Meta- Genomes Proteins Genomes Craig Ventor Dramatization
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Modern Biology Goal New Tool From Phenotype to Genotype Re-sequencing Mapping From Genotype to Phenotype Mutant Collections RNAi From Protein to Function B asic L ocal A lignment S earch T ool From Function to Protein Candidate genes Meta-genome analysis Organism specifc DNA
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From Phenotype to Gene Old Way New Way I New Way II White Rudimentary Yellow C G Disease L288V Visible Markers DNA Markers & Scanning Re-Sequencing A G + C T +
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S ingle N ucleotide P olymorphisms http://www.hapmap.org/index.html Over 10,000 described SNPs in the human genome On average, one site per 1,200 base pairs varies between any two individuals Haplotypes are also useful in mapping SNPs are not the only type of polymorphism
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From Genotype to Phenotype Old Way New Way I New Way II 113 115 114 Directed Mutant Mutant Collection RNA interference Kan R 116 A G T T C A
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Protein Biochemistry Old Way New Way Old Way New Way Activity BLAST Does my protein a) Bind Mg++ b) Digest DNA c) Turn colors d) Kill host cells e) Disappear in mutant X My protein Shigella toxin Vibrio toxin Helicase Protease Kinase Purification Candidates Kinase From Protein to Function From Function to Protein
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Meta-Genomics Before After Small % known Large % known E. coli Unknown H. pylori Unknown E. coli L. casei H. pylori E. cloacae
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Human Genetic Disease From Phenotype to Genotype Over 4,000 described genetic diseases About 10% of adults have a recognized genetic disorder Some genetic diseases affect one person in a million, others one in a few hundred Many diseases are multigenic
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Genetic Counseling? My Aunt has hemophilia, but her sons do not.
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L8 - Lab 7 - Bioinformatics - Bioinformatics and NCBI Dr...

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