Review of Course Topics

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Review of Course Topics

• (Lecture for CS397-CXZ Algorithms in
  Bioinformatics)
• May 5, 2004
• ChengXiang Zhai
• Department of Computer Science
• University of Illinois, Urbana-Champaign

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Key Algorithms

• Pairwise alignment
• Global Needleman-Wunsch
• Local Smith-Waterman
• Multiple sequence alignment
• Exact Multidimensional dynamic programming
• Inexact Feng-Doolittle progressive alignment
• Hidden Markov models
• Finding most likely path Viterbi
• Computing sequence probabilities
  Forward/Backward
• Microarray data analysis
• Agglomerative Hierarchical Clustering
  Single-link, complete-link, avg/group link
• K-means clustering
• Phylogenetic tree construction
• Neighbor-joining
• Maximum parsimony
• Pattern mining
• Deterministic SPLASH
• Sampling Gibbs Sampler
• RNA structure analysis