UVA CS 302 - Computing Genomes, Genomes Computing (42 pages)

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Computing Genomes, Genomes Computing



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Computing Genomes, Genomes Computing

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Pages:
42
School:
University Of Virginia
Course:
Cs 302 - Theory of Computation

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Class 26 Computing Genomes Genomes Computing David Evans http www cs virginia edu evans cs302 Theory of Computation University of Virginia Computer Science Final Exam Sneak Preview Handout available now Honor policy you may discuss these problems with others and use any resources you want until the Final No notes or other resources may be used during the final Intent is to give you an idea what to expect on the final and a chance to start thinking about some problems Don t attempt to memorize answers need to understand things since the actual questions may be different Lecture 26 Computing Genomes and Vice Versa 2 Menu Computing Genomes PS6 Problem 6 Crash course in biology Busy Beaver result Computing with Genomes Conclusion Lecture 26 Computing Genomes and Vice Versa 3 Genome Assembly Problem In order to assemble a genome it is necessary to combine snippets from many reads into a single sequence The input is a set of n genome snippets each of which is a string of up to k symbols The output is the smallest single string that contains all of the input snippets as substrings Lecture 26 Computing Genomes and Vice Versa 4 DNA Sequence of nucleotides adenine A guanine G cytosine C and thymine T Two strands A must attach to T and G must attach to C Lecture 26 Computing Genomes and Vice Versa 5 G C T A Central Dogma of Biology Translation Transcription DNA RNA Protein Image from http www umich edu protein RNA makes copies of DNA segments RNA describes sequences of amino acids Chains of amino acids make proteins Proteins make us Lecture 26 Computing Genomes and Vice Versa 6 Human Genome 3 Billion Base Pairs Each nucleotide is 2 bits 4 possibilities 3 B pairs 1 byte 4 pairs 750 MB 1 CD 650 MB Every sequence of 3 base pairs one of 20 amino acids or stop codon 21 possible codons but 43 64 possible So really only 750MB 21 64 250 MB Much of it 95 is may be junk doesn t encode proteins but some might be important Lecture 26 Computing Genomes and Vice Versa 7 Human Genome Race



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