129_Lecture5_2014

129_Lecture5_2014 - Sequence Analysis Sequence Analysis...

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1/28/14 1 Sequence’Analysis’ Sequence Analysis: Outline 1. Why do we compare sequences? 2. Sequence comparison: from qualitative to quantitative methods 3. Deterministic methods: Dynamic programming 4. Heuristic methods: BLAST 5. Multiple Sequence Alignment Sequence Analysis 1. Why do we compare sequences? 1. Biological sequences 2. Homology vs analogy 3. Homology: orthology and paralogy 4. Applications 2. Sequence comparison: from qualitative to quantitative methods 3. Deterministic methods: Dynamic programming 4. Heuristic methods: BLAST 5. Multiple Sequence Alignment
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1/28/14 2 Similarity:’Homology’vs’Analogy’ Homology: Similarity in characteris3cs resul3ng from shared ancestry. Analogy: The similarity of characteris3cs between two species that are not closely related; a>ributable to convergent evolu3on. Two sisters: homologs Two Elvis : analogs http://evolution.berkeley.edu/evolibrary/search/topicbrowse2.php?topic_id=55 Useful link: Similarity:’Homology’vs’Analogy’ Classical example of homology: Legs and Limbs Koonin EV (2005). Orthologs, paralogs, and evolutionary genomics . Annu. Rev. Genet. 39:309-338. Further reading: Homologous’sequences’are’orthologous’if’they’were’separated’by’a’ specia<on’event’ Orthology: Homologous’sequences’are’paralogous’if’they’were’separated’by’a’ gene’duplica<on’event’ Paralogy: Similarity’in’characteris<cs’resul<ng’from’shared’ancestry. Homology: Homology:’Orthologs’and’Paralogs’
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1/28/14 3 Homology:’Orthologs’and’Paralogs’ Sequencing’projects,’assembly’of’sequence’data’ Evolu<onary’history’ Iden<Fca<on’of’func<onal’elements’in’sequences’ gene’predic<on’ ClassiFca<on’of’proteins’ Compara<ve’genomics’ RNA’structure’predic<on’ Protein’structure’predic<on’ Health’Informa<cs’ Applica<ons’of’Sequence’Analysis’ Sequence Analysis 1. Why do we compare sequences? 2. Sequence comparison: from qualitative to quantitative methods 1. Sequence composition 2. Sequence comparison: DotPlot 3. Sequence alignment 3. Deterministic methods: Dynamic programming 4. Heuristic methods: BLAST 5. Multiple Sequence Alignment
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1/28/14 4 DNA’sequence:’Chargaf s’rules’ Rule 1: In double stranded DNA, the amount of guanine is equal to cytosine and the amount of adenine is equal to thymine (basis of Watson Crick base pairing) Rule 2: the composition of DNA varies from one species to another; in particular in the relative amounts of A, G, T, and C bases DNA’sequence:’Chargaf s’rules’ Comparing sequences based on their tri-peptide content Proteins: Structure, Function and Genetics 54 , 20-40 (2004)
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1/28/14 5 DotPlot:’Overview’of’Sequence’Similarity’ Build a table S: - rows: Sequence 1 - columns: Sequence 2 Assign a score S(i,j) to each entry in the table: - select a window size WS WS WS i j - Compare window around i with window around j -> Score(i,j) Display table of scores S - show a dot at position (i,j) if Score(i,j) > Threshold
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129_Lecture5_2014 - Sequence Analysis Sequence Analysis...

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