Introduction to Bioinformatics

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 (
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?

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