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UC Davis Academics

Fundamental Algorithms in Bioinformatics

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32 items
Last updated on Jul 16, 2015
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This course covers fundamental algorithms for efficient analysis of biological sequences and for building evolutionary trees. This is an undergraduate course taught by UC Davis computer science professor Dan Gusfield focusing on the ideas and concepts behind the most central algorithms in biological sequence analysis. Dynamic Programming, Alignment, Hidden Markov Models, Statistical Analysis are emphasized.
UC Davis Academics
Lecture 1: Introduction to bioinformatics and the course
47:30
Lecture 1: Introduction to bioinformatics and the course

UC Davis Academics
Lecture 2: Further introduction
48:43
Lecture 2: Further introduction

UC Davis Academics
Lecture 3: Defining sequence similarity
51:07
Lecture 3: Defining sequence similarity

UC Davis Academics
Lecture 4: Extending the model of sequence similarity
48:01
Lecture 4: Extending the model of sequence similarity

UC Davis Academics
Lecture 5: Computing sequence similarity
47:44
Lecture 5: Computing sequence similarity

UC Davis Academics
Lecture 6: Computing similarity using an alignment graph
48:00
Lecture 6: Computing similarity using an alignment graph

UC Davis Academics
Lecture 7: From alignment graphs to formal dynamic programming
1:09:00
Lecture 7: From alignment graphs to formal dynamic programming

UC Davis Academics
Lecture 8: Sequence alignment using dynamic programming - continued
49:33
Lecture 8: Sequence alignment using dynamic programming - continued

UC Davis Academics
Lecture 9: Local sequence alignment
46:18
Lecture 9: Local sequence alignment

UC Davis Academics
Lecture 10: End-gap-free alignment and whole-genome shotgun sequencing
51:07
Lecture 10: End-gap-free alignment and whole-genome shotgun sequencing

UC Davis Academics
Lecture 11a: Expected Length of the Longest Common Subsequence
12:38
Lecture 11a: Expected Length of the Longest Common Subsequence

UC Davis Academics
Lecture 11b: Expected Length of the Longest Common Substring
29:31
Lecture 11b: Expected Length of the Longest Common Substring

UC Davis Academics
Lecture 12: Expected longest common substring II
16:02
Lecture 12: Expected longest common substring II

UC Davis Academics
Lecture 13: Probability of a complete query match in a database
40:27
Lecture 13: Probability of a complete query match in a database

UC Davis Academics
Lecture 14: BLAST I
50:40
Lecture 14: BLAST I

UC Davis Academics
Lecture 15: BLAST II
46:28
Lecture 15: BLAST II

UC Davis Academics
Lecture 16: BLAST statistics
9:59
Lecture 16: BLAST statistics

UC Davis Academics
Lecture 17: Probability and database search
44:55
Lecture 17: Probability and database search

UC Davis Academics
Lecture 18: Multiple sequence alignment I
50:39
Lecture 18: Multiple sequence alignment I

UC Davis Academics
Lecture 19: Multiple sequence alignment II
50:33
Lecture 19: Multiple sequence alignment II

UC Davis Academics
Lecture 20: Multiple sequence alignment III
49:52
Lecture 20: Multiple sequence alignment III

UC Davis Academics
Lecture 21: Uses of multiple sequence alignment
41:15
Lecture 21: Uses of multiple sequence alignment

UC Davis Academics
Lecture 22: From profiles to Markov models
48:30
Lecture 22: From profiles to Markov models

UC Davis Academics
Lecture 23: Hidden Markov models
49:25
Lecture 23: Hidden Markov models

UC Davis Academics
Lecture 24: Hidden Markov models and the Vitterbi algorithm
49:55
Lecture 24: Hidden Markov models and the Vitterbi algorithm

UC Davis Academics
Lecture 25: From the Vitterbi algorithm to the forward algorithm
45:46
Lecture 25: From the Vitterbi algorithm to the forward algorithm

UC Davis Academics
Lecture 26: Hidden Markov models - The Backwards algorithm
28:22
Lecture 26: Hidden Markov models - The Backwards algorithm

UC Davis Academics
Lecture 27: Introduction to evolutionary trees - Ultrametric trees
20:51
Lecture 27: Introduction to evolutionary trees - Ultrametric trees

UC Davis Academics
Lecture 28: Algorithms for Ultrametric trees - molecular clocks
37:49
Lecture 28: Algorithms for Ultrametric trees - molecular clocks

UC Davis Academics
Lecture 29; Additive trees and the Neighbor-Joining algorithm
47:18
Lecture 29; Additive trees and the Neighbor-Joining algorithm

UC Davis Academics
Lecture 30: Maximum Parsimony and minimum mutation methods
39:04
Lecture 30: Maximum Parsimony and minimum mutation methods

UC Davis Academics
Postscript: Where to go next
4:50
Postscript: Where to go next