lec04 - CSE 427 Computational Biology Winter 2008 Sequence...

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1 CSE 427 Computational Biology Winter 2008 Sequence Alignment; DNA Replication
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3 Sequence Alignment Part I Motivation, dynamic programming, global alignment
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4 Sequence Alignment What Why A Simple Algorithm Complexity Analysis A better Algorithm: “Dynamic Programming”
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5 Sequence Similarity: What G G A C C A T A C T A A G T C C A A T
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6 Sequence Similarity: What G G A C C A T A C T A A G | : | : | | : T C C – A A T
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7 Sequence Similarity: Why Most widely used comp. tools in biology New sequence always compared to sequence data bases Similar sequences often have similar origin or function Recognizable similarity after 10 8 –10 9 yr
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8 Taxonomy Report root . ................................ 64 hits 16 orgs . Eukaryota . ......................... 62 hits 14 orgs [cellular organisms] . . Fungi/Metazoa group . ............. 57 hits 11 orgs . . . Bilateria . ..................... 38 hits 7 orgs [Metazoa; Eumetazoa] . . . . Coelomata . ................... 36 hits 6 orgs . . . . . Tetrapoda . ................. 26 hits 5 orgs [;;; Vertebrata;;;; Sarcopterygii] . . . . . . Eutheria . ................ 24 hits 4 orgs [Amniota; Mammalia; Theria] . . . . . . . Homo sapiens . .......... 20 hits 1 orgs [Primates;; Hominidae; Homo] . . . . . . . Murinae . ............... 3 hits 2 orgs [Rodentia; Sciurognathi; Muridae] . . . . . . . . Rattus norvegicus . ... 2 hits 1 orgs [Rattus] . . . . . . . . Mus musculus . ........ 1 hits 1 orgs [Mus] . . . . . . . Sus scrofa . ............ 1 hits 1 orgs [Cetartiodactyla; Suina; Suidae; Sus] . . . . . . Xenopus laevis . .......... 2 hits 1 orgs [Amphibia;;;;;; Xenopodinae; Xenopus] . . . . . Drosophila melanogaster . ... 10 hits 1 orgs [Protostomia;;;; Drosophila;;;] . . . . Caenorhabditis elegans . ...... 2 hits 1 orgs [; Nematoda;;;;;; Caenorhabditis] . . . Ascomycota . .................... 19 hits 4 orgs [Fungi] . . . . Schizosaccharomyces pombe . ... 10 hits 1 orgs [;;;; Schizosaccharomyces] . . . . Saccharomycetales . ........... 9 hits 3 orgs [Saccharomycotina; Saccharomycetes] . . . . . Saccharomyces . ............. 8 hits 2 orgs [Saccharomycetaceae] . . . . . . Saccharomyces cerevisiae . 7 hits 1 orgs . . . . . . Saccharomyces kluyveri . .. 1 hits 1 orgs . . . . . Candida albicans . .......... 1 hits 1 orgs [mitosporic Saccharomycetales;] . . Arabidopsis thaliana . ............ 2 hits 1 orgs [Viridiplantae; …Brassicaceae;] . . Apicomplexa . ..................... 3 hits 2 orgs [Alveolata] . . . Plasmodium falciparum . ......... 2 hits 1 orgs [Haemosporida; Plasmodium] . . . Toxoplasma gondii . ............. 1 hits 1 orgs [Coccidia; Eimeriida; Sarcocystidae;] . synthetic construct . ............... 1 hits 1 orgs [other; artificial sequence] . lymphocystis disease virus .
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This note was uploaded on 04/22/2008 for the course CSC 427 taught by Professor Ruzzo during the Winter '08 term at University of Washington.

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lec04 - CSE 427 Computational Biology Winter 2008 Sequence...

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