pairwise(alignment · 2015. 9. 9. · most common use ofpairwise sequence alignments is to search...
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Pairwise Alignment
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Searching for the op5mal alignment…
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Solu5on: Dynamic programming
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TCGCA TCCA
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Filling a scoring matrix
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What did you learn?
• Purpose of sequence alignment: • Find evolu5onary rela5onships • Predict protein func5on
• The op5mal alignment can be found using dynamic programming: • Local alignment: Smith-‐Waterman • Global alignment: Needleman-‐Wunsch
• Op5mal alignment means having the best possible score given: 1. Subs5tu5on matrix 2. Set of gap penal5es
• The op5mal alignment is NOT necessarily the most biologically meaningful
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Exercise 1 – Pairwise Alignment
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Database Searching
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What did you learn?
• Heuris5c methods (e.g. BLAST) is faster to search databases than Smith-‐Waterman
• BLASTN, BLASTP etc.
• E-‐value: Measure for significance of database hit
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Exercise 2 – Using BLAST