Class 42 - BLASTING AND CHIPPING THE SCIENCE OF FINDING...

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Unformatted text preview: BLASTING AND CHIPPING THE SCIENCE OF FINDING THINGS IN GENOMES IN THE 21ST CENTURY A few reminders! 1. Please answer the end of year survey by 11 pm tonight (it is worth 7 pts): http://www.colorado.edu/sei/surveys/ Fall08/CLASSfa08-mcdb-2150-post.htm 2. Michelle would like to take a few pictures of students using clickers. It would be great if some of you would be willing to stay for a few minutes after class. Thanks! BLAST ET AL . BLAST AND ITS RELATIVES ALLOW RAPID SEARCHING OF GENOME DATA (DNA/PROTEIN) OTHER SOFTWARE ALLOWS VIEWING “VALUE-ADDED” GENOMIC DATA PROTEINS STRUCTURES MAPS - RESTRICTION, GENETIC, PHYSICAL EXPRESSION - LEVELS, INTERACTIONS WHAT ARE THE DATA THOUGH? US (NIH), EUROPE (EMBL), JAPAN(RIKEN) ESTABLISHED REPOSITORIES THAT ARE FREE!! JOURNALS COOPERATE BY REQUIRING ALL SEQUENCING AND MAPPING DATA TO BE DEPOSITED MANY UNIVERSITIES, AND SOME COMPANIES ALSO MAINTAIN VALUE-ADDED SITES UCSC - MOUSE/HUMAN (HTTP://GENOME.UCSC.EDU ) AFFYMETRIX - SNP DATA (HTTP://WWW.AFFYMETRIX.COM ) WHAT CAN YOU SEARCH FOR? NEARLY ANYTHING! TEXT SEQUENCES REFERENCES ID NUMBERS MAILING ADDRESSES! HOW MUCH DATA A BLEEPIN’ TON!! CURVES CONTINUE TODAY - ROUGHLY EXPONENTIALLY THE OTHER BIG TECHNOLOGY HIGH THROUGHPUT EXPRESSION ANALYSIS “CHIPS” PIONEERED BY PAT BROWN/DAVID BOTSTEIN STANFORD COULD PLACE THOUSANDS OF “PROBES” ON A SINGLE GLASS SLIDE - HYBRIDIZE TO LABELED RNA ALLOWS SIMULTANEOUS QUANTITATION OF ALL EXPRESSED SEQUENCES IN A CELL ORIGINAL DNA SPOTTER MODIFIED FROM AN INKJET PRINTER!! ENHANCED IMAGE OF OUTPUT THE INTENSITY HAS THE INFO TO COMPARE ONE CONDITION WITH ANOTHER COLORS CAN BE MIXED EACH COLOR DETECTED SEPARATELY, COLORED BY INTENSITY Please answer this question without talking to your neighbor Mix and hybridize to chip...
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Class 42 - BLASTING AND CHIPPING THE SCIENCE OF FINDING...

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