MMG 433: Review/Study Guide
Two approaches to Genomics:
Philosophical – New way to approach biological problems
Practical – High throughput methods for analyzing biological systems
1392 complete bacterial genomes currently in Entrez Genome database; >3500 draft
genomes in database, prob. 50K done but not deposited. New sequencing methods on the horizon: Goal –
1000 human genome, $1 bacterial genome, Genetic mapping in bacteria – obsolete, PacBio=10Gb/hr
2-D gel electrophoresis
: Determine the function of every gene in a genome. Determine the genes
essential for life; Minimal genome concept, Mycoplasma – 500 genes, 256 genes estimate for life – can
we build a bacterium?
The Informatics Problem:
There are approximately 106,633,156,756 bases in 108,431,692 sequence records in the
traditional GenBank divisions and 148,165,117,763 bases in 48,443,067 sequence records in the WGS
division as of August 2009
Over 50 Million PubMed searches are preformed
Microarrays, proteomics, networks
How is this much data handled?
Lab 1: NCBI, PubMed tutorials, familiarize with Macbooks.
-old view (
): Single chromosome, Circular, Replication initiates from a single fixed origin, little or
no horizontal gene transfer.
-new view: Bacteria can contain more than one chromosome, Bacterial chromosomes can be linear,
Horizontal gene transfer is common, expect the unexpected.
-4 bases: AGCT