CSE / BMMB 566, Spring 2019 Algorithms and Data Structures in Bioinformatics
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TopicAnnouncements / HandoutsReferences
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CSE / BMMB 566, Spring 2019, Algorithms and Data Structures in Bioinformatics
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Instructor: Paul Medvedev (pzm11)
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Link to Syllabus
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Link to Canvas page
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Completed Lectures
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1/7/19Class intro and bio background
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1/11/19Knuth-Morris-Pratt algorithmhttp://jakeboxer.com/blog/2009/12/13/the-knuth-morris-pratt-algorithm-in-my-own-words/
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1/14/19KMP continued, Suffix triesProgramming Assignment 1 dueGusfield Ch 2.2, Haubold and Wiehe, Chapter 3
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1/16/19Suffix trees
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Scheduled Lectures
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1/18/19no classes
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1/21/19MLK day, no classes
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1/23/19(tent) suffix trees, suffix arrays
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1/25/19(tent) BWTHomework 2 is duehttps://www.youtube.com/watch?v=4n7NPk5lwbI
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1/28/19
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1/30/19
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2/1/19
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2/4/19
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2/6/19
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2/8/19
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2/11/19
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2/20/19
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2/22/19
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2/25/19
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2/27/19
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3/1/19
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3/4/19 - 3/9/19Spring break, no class
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3/11/19
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3/13/19
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3/15/19
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3/18/19
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3/20/19
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3/22/19
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3/25/19
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3/27/19
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3/29/19
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4/1/19
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4/5/19
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4/22/19
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4/24/19
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4/26/19
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Remaining topics (tenative)
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FM-index and Sequence AlignmentHaubold and Wiehe, subset of Chapter 2.
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http://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm
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Needleman-Wunsch, Smith Waterman
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Gotoh's algorithm and Linear-space alignmentHirschberg's original paper (see canvas)
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http://en.wikipedia.org/wiki/Hirschberg%27s_algorithm
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Four Russians Speed-up / Heuristic Pairwise alinmentGusfield, Ch 12.7 (see canvas)
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Mutliple Sequence AlignmentHaubold and Wiehe, Chapter 4, http://mummer.sourceforge.net/MUMmer.pdf
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Structural Variation Detection
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Structural Variation Detection / Modeling Biological Problems
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Modeling Biological Problems
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Modeling Biological Problems / Genome Assemblyhttps://arxiv.org/pdf/1706.05429
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Genome assembly
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Hidden Markov Models
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Hidden Markov Models
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Hidden Markov Models
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Profile HMMs
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Phylogeny introduction, UPGMAChapter 7 of Durbin et al. book
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Phylogeny (neighbor joining)
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Phylogeny (Fitch's algorithm, Sankoff's)
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