Genetics 3301

Chapter 12: Genomics

Genomic Analysis:

Ä Genomics - Why study whole genomes?; Bioinformatics; comparative genomics; functional genomics.

Ä Generating a genome sequence map (12-2); Levels of completeness in draft and finished products; Problems encountered due to repetitive sequences.

Ä Whole genome shotgun sequencing (WGS); Sequencing simple genomes; Use of paired end reads to assemble complex genome sequences (12-4, 12-5, 12-6); Generating a physical map of ordered clones to sequence a whole genome (12-8).

Identifying genes:

Ä Using molecular markers to generate a linkage map; Mapping using RFLPs (12-10); Mapping using SSLP markers ≠ minisatellite and microsatellite (12-12).

Ä Placing molecular markers on cytogenetic maps using FISH analysis (12-14); Attaching molecular markers to physical and genomic sequence maps (12-17).

Ä Identifying a gene of interest within a genomic sequence map using the candidate gene approach(12-18).

Bioinformatics:

Ä Information content in the genome (12-19); ORF detection via comparison with EST sequences (12-20); Identifying genes by detecting consensus protein binding sites in genomic sequence (12-21); Identifying genes using BLAST protein and DNA sequence comparisons.

Functional genomics:

Ä The transcriptome (12-27); The proteome; The interactome; The phenome.

Key terms: Know all of these except chromosome painting, comparative genomics; minimum tiling path; reporter gene, scaffold, structural genomics, supercontig, systems biology, two-hybrid test.

Problems: 2, 3, 6, 12, 18, 29, 37.