This module studies algorithms for most important computational problems in genomics. We shall study exact algorithms for those problems that can be solved easily and approximation and/or heuristic algroithms for those difficult problems. The topics that will be covered include

• Genomics primer: Nucleic acids, genes, proteins, genomes;
• Sequence comparisons: Global alignment, local alignment, and BLAST tools;
• Multiple sequence alignments: scoring a multiple alignment, dynamic approach, approximation approach, Feng-Doolittle algorithm;
• Phylogenetic analysis: Parsimony, distance-based methods, maximum likelihood, PAUP and PHYLIP tools;
• DNA sequence assembly and mapping: Human Genome Project, sequence assembly, restriction mapping, physical mapping;
• (Optional) Gene prediction, finding long ORF's, detecting promoter regions, splice alignment;
• (Optional) Protein structure and drug design.