On this page you will find copies of the handouts and summary information for each lecture. You will also find the question of the day and a listing of any assignments handed out during that lecture. Notes for each lecture are not provided--you must take your own. While sample lecture notes are given at the textbook website, exams will also include additional topics discussed only in class.

Lecture 1 - February 2
Summary	An introduction to the course and to basic molecular biology.
QOTD	What are some advantages to having RNA as an intermediary between the genetic source (DNA) and the functional element (protein) in the cell?
Handouts	Computational Questionnaire (Due Feb. 3) Room 122 Access Application (Due Feb. 3) Nucleic Acid Structures

Lecture 2 - February 3
Summary	How to use the computers and python.
Reading	Python Tutorial, sections 1-5 and 7
QOTD	How would you write a program to calculate the value of 10 factorial (that is, 10*9*8* ... * 1)?
Handouts	Handy UNIX Command List Supplemental Programming Info
Files	Python Examples (l02-examples.py) Solution to QOTD

Lecture 3 - February 9
Summary	Accessing information through the NCBI website.
Reading	Chapters 1, 2
Optional Reading	Brenner, S.E. (1999) “Errors in Genome Annotation.” Trends in Genetics 15 (4): 132-3. [PDF]
QOTD	What is the protein sequence of the human gene p53? Why is this gene relevant?

Lecture 4, Part 1 - February 16
Summary	Pairwise sequence alignment.
Reading	Chapter 3
QOTD	In a PAM matrix, the cell for a mutation from Val to Ile has a value of 0.15. What does this number mean?

Lecture 4, Part 2 - February 17
Summary	Pairwise sequence alignment.
Reading	Chapter 3
QOTD	What are the key differences between global and local sequence alignment?
Handouts	Worked Needleman-Wunsch Example

Lecture 5 - February 23
Summary	BLAST Searching
Reading	Chapter 4
QOTD	What factors affect the number of results returned by a BLAST search?

Lecture 6 - February 24
Summary	Advanced BLAST Searching
Reading	Chapter 5
QOTD	What are the differences between PHI- and PSI- BLAST?

Lecture 7 - March 2
Summary	Gene Expression and Microarrays
Reading	Chapter 6
QOTD	How would you design an experiment to determine the effects of a particular drug on tumor cells grown in culture? To what aspects of the gene expression setup would you have to pay particular attention?

Lecture 8 - March 10
Summary	Protein Structure
Reading	Chapter 9
QOTD	How many possible backbone conformations exist for a peptide chain of length 10?

Lecture 9 - March 30
Summary	Proteomics
Reading	Chapter 8
QOTD	Why might the predictions made from a hydropathy plot be inaccurate?

Lecture 10 - April 6
Summary	Multiple Sequence Alignment
Reading	Chapter 10
QOTD	What aspects of ClustalW might cause your seqeunce alignment to be sub-optimal?

Guest Lecture - April 13
Summary	Protein Structure Prediction (George Rose)
Reading	Bradley, P., Misura, K. S. M., and Baker, D. (2005) “Toward High-Resolution de Novo Structure Prediction for Small Proteins.” Science 309 (5742): 1868-1871. [PDF]

Lecture 11 - April 20
Summary	Molecular Evolution and Genome Analysis
Reading	Chapters 11, 12
Optional Reading	Sanger Dideoxynucleotide Sequencing
QOTD	When might a distance-based tree be better than a maximum parsimony tree?

Lecture 12 - April 27
Summary	The Human Genome
Reading	Chapter 17
QOTD	What limitations currently exist on the full potential of knowing the human genome?

Lecture 13 - April 28
Summary	Bioinformatics and Human Disease
Reading	Chapter 18
QOTD	How would you determine whether a single-nucleotide polymorphism was responsible for a specific disorder?