Bioinformatics Algorithms: Lecture 27 - Last Lecture, Study notes of Computer Science

Download Bioinformatics Algorithms: Lecture 27 - Last Lecture and more Study notes Computer Science in PDF only on Docsity! CMSC 858E Lecture 27: Last lecture!!!! 12/12/06 • Z algorithm • Boyer-Moore: bad character rule, good suffix rule, proof of linearity • KMP • Aho-Corasick: many patterns, don’t care symbols • Suffix trees: Ukkonen’s construction, applications • Inexact alignment: dynamic programming, speed-up/memory reduction heuristics • Multiple alignments: exact solution, progressive alignment, sum of pairs score, star score, Steiner score, phylogenetic alignment, consensus score • Phylogenetic trees: scoring, distance methods (neighbor joining, UPGMA), maximum likelihood • RNA folding: dynamic programming solution, covariance models • Protein folding: folding on a lattice, threading