Expected accuracy sequence alignment Usman Roshan Optimal pairwise alignment Sum of pairs (SP) optimization: find the alignment of two sequences that maximizes the similarity…

Hidden Markov Models Usman Roshan CS 675 Machine Learning HMM applications Determine coding and non-coding regions in DNA sequences Separating âbadâ pixels from âgoodâ…

Hidden Markov Models BMI/CS 776 www.biostat.wisc.edu/~craven/776.html Mark Craven [email protected] March 2002 Announcements talks this week Quantitative Genetics in…

Maximum Likelihood (ML) Parameter Estimation with applications to inferring phylogenetic trees Comput. Genomics, lecture 7a Presentation partially taken from Dan Geiger,…

. Phylogenetic Trees Lecture 11 Sections 6.1, 6.2, in Setubal et. al., 7.1, 7.1 Durbin et. al. © Shlomo Moran, based on Nir Friedman. Danny Geiger, Ilan Gronau shlomo moran…

. Sequence Alignment I Lecture #2 This class has been edited from Nir Friedman’s lecture which is available at www.cs.huji.ac.il/~nir. Changes made by Dan Geiger, then…

Phylogenetic Trees (2) Lecture 12 Based on: Durbin et al Section 7.3, 7.8, Gusfield: Algorithms on Strings, Trees, and Sequences Section 17. - fall 05-6: went quite slowly…

EM algorithm and applications Lecture #9 Background Readings: Chapters 11.2, 11.6 in the text book, Biological Sequence Analysis, Durbin et al., 2001. - חרף 04-5: הספקתי…

Covariance in RNA ref Covariance Mij= Sfxixjlog2[fxixj/(fxifxj)] M=0 to 2 bits; x=base type xixj see Durbin et al p. 266-8. D-stem anticodon TyC 3’acc Mutual Information…

Advanced Algorithms and Models for Computational Biology Class Overview Eric Xing & Ziv Bar-Joseph Lecture 1, January 18, 2005 Reading: Chap. 1, DTM book Logistics Class…