Statistics 590C (Bioinformatics II)

Instructor:  Jeff Thorne


Monday, Wednesday, and Friday:  11:45A.M.-12:35P.M.

Classroom: 461 Riddick Hall



Syllabus
Pairwise Alignment Review (file "bioinfintrolecture2017.pdf")
Introduction / Background on Likelihood-Based Inference (file "basicbayesandml.pdf")
Lecture Notes on Markov models (pages 1-21, file "markov.pdf")
Lecture Notes on basic HMM algorithms (pages 22-28, file "markov2.pdf")
Lecture Notes on underflow (pages 29-31, file "markov3.pdf")

Lecture Notes on HMM miscellanea (pages 32-40, file "HMMmisc.pdf")

Lecture Notes on some assorted databases (pages 41-49, file "databases2017.pdf")


Lecture Notes on miscellaneous fold recognition and CASP issues (pages 50-62, file "protstructandcasp2017.pdf")
Supplementary Notes on protein tertiary structure and CASP to be distributed in hard copy form


A quick tour of some techniques for obtaining random samples (pages 63-82, file "sampling2017.pdf")


An overview of Gibbs Sampling (pages 83-91, file "gibbs2017.pdf")


Dirichlet distribution and pseudocounts (pages 92-97, file "dirichlet2017.pdf")

Notes on RNA secondary structure prediction were distributed in hard copy form


A little about evolutionary models and the EM algorithm (pages 98-125, file "evomodel2017.pdf")

Reading Assignments



Homework #1



Homework #2



Homework #4



Homework #5