CSE 40532 Oakland University

Sequence alignment (continued) Global Alignment (review) Input: Two strings, labeled s and t |s| is n |t| is m Output: Two strings sA and tA such that: sA and tA are of equal length L Characters must be in same order, with \"-\" spacers as need

Parsimony Review Three types of tree construction Distance: find tree that accounts for observed distances Parsimony: find tree that requires minimum # of changes Maximum likelihood: tree that maximizes likelihood of data 1 Review UPGMA This

Lecture 9 Intro to Hidden Markov Models Big questions from last time Evaluation How likely is a sequence given a model? More formally, given a model M and a sequence s, find Pr(x | M). Decoding (or inference) Given a sequence and a model, try

Lecture 7 Intro to Hidden Markov Models Markov models, revisited We can also view Markov models as a discrete (finite) system: N total states Start at some initial state (t = 1) based on multinomial model System proceeds to the next state based

Computational Problems in Genomics Scott Emrich Computer Science and Engineering University of Notre Dame August 26, 2008 1 Biology easily has 500 years of exciting problems to work on -Donald E. Knuth August 26, 2008 2 News: Allergy free cats

Ab initio gene finding Introduction Gene A sequence of nucleotides that are translated into proteins Gene prediction Given the model of a gene above, determine the beginning and end positions of all genes in a genome. 1 Central dogma of molec

Variation within and between species Ch 5 Most recent common ancestor of humans via mitochondrial DNA Passed from mother to child She is believed to have lived about 140,000 years ago in what is now Ethiopia, Kenya or Tanzania. Source: Newsweek 111

CSE40532 Bioinformatics computing Lecture #2 DNA sequencing has been around since the late 1970s, but a big genome was not completed until 1995 by The Institute for Genomic Research (TIGR) headed by Dr. Craig Venter. Big in biology context was a fre

Phylogenetics The basics In general, the closer the two species are evolutionarily, the closer their genomes will be We assume all life comes from a common ancestor Relationships can be illustrated using trees Phylogenetics\' task is to infer the