Course Description
Computational approaches to the study of properties of eukaryotic and prokaryotic genomes, genome evolution, and statistical and computational methods for genome analyses and comparisons. Topics include composition of prokaryotic genomes, eukaryotic chromosome structure, lateral gene transfer, genome rearrangements. Emphasis will be placed on biological interpretations of sequence data.
Athena Title
GENOME ORGANIZATION
Semester Course Offered
Offered spring
Grading System
A - F (Traditional)
Course Objectives
The course participants will acquire (i)basic skills in the use of computational tools, databases and statistical techniques for analyses and comparisons of genomic DNA sequences, and (ii) knowledge about organization, content, and evolution of genomes. The course is designed to make the computational and statistical methods accessible to students with primary background in biology by emphasizing specific tasks of genome analysis and biological interpretations of the results rather than detailed technical aspects of the methods and algorithms. Students will be required to present papers from the primary literature to the class for further discussion. By the end of the course the students should be able to: (1) Analyze, compare, and interpret properties of genomic DNA sequences (2) Distinquish unique characteristics of genomic nucleotide sequences from common or universal characteristics (3) Apply statistical methods and computational tools for genome sequence analysis and properly interpret their results
Topical Outline
Overview of online resources and basic Linux shell commands Composition of prokaryotic genomes Methods for analysis of sequence heterogeneity Biased codon usage, relationship to gene expression levels Identification of genomic islands, pathogenicity islands and lateral gene transfer events Genome rearrangements, evolutionary conservation of gene order DNA linguistics Types, distributions and roles of repeats DNA curvature, sequence periodicity analysis Special sequence patterns and DNA conformation Relationship between organism's habitat, metabolism and genome/proteome composition Composition of eukaryotic genomes Eukaryotic chromosome structure Evolution of eukaryotic genomes SNPs and linkage disequilibrium, the human HapMap project Abnormal genomic structure and disease