Fundamental Algorithms in Bioinformatics

Latest Episodes:

Lecture 29; Additive trees and the Neighbor-Joining algorithm Jan 30, 2010

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Additive trees and their construction. The Neighbor-Joining algorithm and its use with near-additive data. Bootstrap values and their misuse.

Lecture 28: Algorithms for Ultrametric trees — molecular clocks Jan 29, 2010

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Algorithms for constructing an Ultrametric Tree from an Ultrametric Matrix, and the relationship of ultrametrics to the molecular clock.

Lecture 27: Introduction to evolutionary trees - Ultrametric trees Jan 28, 2010

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lntroduction to trees that represent evolution. We start with the case of perfect data: the Ultrametric tree case.

Lecture 26: Hidden Markov models - The Backwards algorithm Jan 27, 2010

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What the Backwards algorithm computes and why we want it. Profile HMMs and their use. Cleaning up some topics in sequence analysis (running out of time); PSI-BLAST and its dangers.

Lecture 25: From the Vitterbi algorithm to the forward algorithm Jan 26, 2010

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This class finishes the discussion of the Vitterbi algorithm, its time analysis and the traceback algorithm. Introduction to the Forward algorithm to compute the probability that a given sequence is generate by the HMM.

Lecture 24: Hidden Markov models and the Vitterbi algorithm Jan 25, 2010

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Finish the discussion of HMMs for CpG islands. Introduction to the Vitterbi algorithm (really dynamic programming) to find the most likely Markov Chain generating a given sequence.

Lecture 23: Hidden Markov models Jan 24, 2010

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Hidden Markov models to identify CpG islands. This lecture follows the discussion in Durbin and Eddy.

Lecture 22: From profiles to Markov models Jan 23, 2010

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Finish the discussion of profiles and log-odds ratios. introduction to Markov Models and Hidden Markov Models

Lecture 21: Uses of multiple sequence alignment Jan 22, 2010

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Use of multiple sequence alignment to build a model of a set of biologically related sequences. Profiles, log-odds ratios.

Lecture 20: Multiple sequence alignment III Jan 21, 2010

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The center tree method and analysis; progressive alignment, guide trees, CLUSTAL, uses of multiple alignment