1. http://cs273a.stanford.edu [Bejerano Aut08/09] 1 MW 11:00-12:15 in Beckman B302 Profs: Serafim Batzoglou, Gill Bejerano TA: Cory McLean

2. http://cs273a.stanford.edu [Bejerano Aut08/09] 2 Lecture 6 Repetitive Sequences Genes Conservation and Function

3. http://cs273a.stanford.edu [Bejerano Aut08/09] 3 Meet Your Genome Continues [Human Molecular Genetics, 3rd Edition]

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5. 5 Repeats / obile Elements ("selfish DNA") Human Genome: 3*10 9 letters 1.5% known function >50% junk

6. http://cs273a.stanford.edu [Bejerano Aut08/09] 6 [Adapted from Lunter]

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15. http://cs273a.stanford.edu [Bejerano Aut08/09] 15 Assemby Challenges

16. http://cs273a.stanford.edu [Bejerano Aut08/09] 16 Inferring Phylogeny Using Repeats [Nishihara et al, 2006]

17. http://cs273a.stanford.edu [Bejerano Aut08/09] 17 Functional elements from obile Elements [Yass is a small town in New South Wales, Australia.] Co-option event, probably due to favorable genomic context All other copies are destined to decay over time at a neutral rate [Bejerano et al., Nature 2006]

18. http://cs273a.stanford.edu [Bejerano Aut08/09] 18 Genome Size Variability 1pg = 978 Mb

19. http://cs273a.stanford.edu [Bejerano Aut08/09] 19 Simple Repeats Every possible motif of mono-, di, tri- and tetranucleotide repeats is vastly overrepresented in the human genome. These are called microsatellites, Longer repeating units are called minisatellites, The real long ones are called satellites. Highly polymorphic in the human population. Highly heterozygous in a single individual. As a result microsatellites are used in paternity testing, forensics, and the inference of demographic processes. There is no clear definition of how many repetitions make a simple repeat, nor how imperfect the different copies can be. Highly variable between genomes: e.g., using the same search criteria the mouse & rat genomes have 2-3 times more microsatellites than the human genome. They’re also longer in mouse & rat.

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24. http://cs273a.stanford.edu [Bejerano Aut08/09] 24 From an evolutionary point of view transposons and simple repeats are very different. Different instances of the same transposon share common ancestry (but not necessarily a direct common progenitor). Different instances of the same simple repeat most often do not.

25. http://cs273a.stanford.edu [Bejerano Aut08/09] 25 The Gene-ome makes < 2% of the H.G. [Human Molecular Genetics, 3rd Edition]

26. http://cs273a.stanford.edu [Bejerano Aut08/09] 26 Gene Finding – The Practice Challenge: “The genes, the whole genes, and nothing but the genes” Problems: spliced ESTs  legitimate gene isoform? predicting gene isoforms tissue/condition-specific genes / gene isoforms single exon genes pseudogenes Practice:

27. http://cs273a.stanford.edu [Bejerano Aut08/09] 27 Evolution of Gene Finding Tools etc