Rationale
This course focuses on the subset of bioinformatics concerned with genome analysis. For this topic to be of more general interest than working out a crossword puzzle, it is necessary to connect the sequences of genomes to the workings of whole organisms. To do this, you need to know molecular biology.

Many of you already have background in molecular biology. For those, a quick review by means of Problem Set 1 may be sufficient.

For the rest, I've supplied below material drawn from the course Molecular Biology Through Discovery and will schedule special weekly sessions to help you get up to speed.

But for both groups, we will be moving on, particularly in areas related to gene regulation and phage biology. See below.

Special Readings, Investigations, and Problem Sets for those who need them
    Notes: Strategies of Life
Graphical Companion: Self Assembly
Problem Set: Problem set concerning Strategies of Life
    Notes: Protein
Tutorial: Hemoglobin structure (Eric Martz, U Massachussetts - Amherst)
Resource: Protein Data Base (protein structures and sequences)
Resource: Protein Explorer (a protein visualization tool)
Resource: FirstGlance in Jmol (a less powerful but simpler protein visualization tool)
Problem Set: Problem set concerning protein
    Notes: DNA Structure (reduced version) or (full strength version)
Investigation: Build your own DNA
Problem Set: Problem set concerning DNA structure
    Notes: DNA Replication
Animation: Polymerase Chain Reaction (basic description)
Animation: Polymerase Chain Reaction (more flash)
Problem Set: Problem set concerning DNA replication
    Notes: Transcription and Translation
Table: The genetic code
Problem Set: Problem set concerning translation

Molecular biology for all
    Investigation: What is a Gene? and companion
    Notes: Gene Regulation and Bacteriophage
    Reading and Tour:
Peter Lynge Madsen, Annette H Johansen, Karin Hammer, and Lone Brondsted
Journal of Bacteriology (1999) 181:7430-7438
The genetic switch regulating activity of early promoters of the temperate lactococcal bacteriophage TP901-1
Tour

Problem Set
    Problem Set 1: Review of Molecular Biology
    Problem Set 2: Molecular Investigations

To Hand In
    18 Jan, end of day*: Responses to questions from What is a Gene?
    21 Jan, end of day*: Problem Set 1
    28 Jan, end of day*: Problem Set 2

* (however you care to define it, within reason)