Assignments for Wednesday's class:

• Read through article from Tillier and Collins on Genome rearrangement by replication-directed translocation (also available on HuskyCT). Try to understand Figure 1 and 2. Can you think of alternative explanations?

Assignment for Friday's class

• Go through blast slides
• Think about how you will transfer files back and forth from the xanadu cluster.

Remark: Some things are only accessible whe you are at a computer inside the UConn domain. The easiest way to have nearly the same access from outside UConn is to use vpn. A link on how-to install JunoPulse is here (note the link for MacOS_X users)

Discussion

PAM versus Blosum

• Which to use for divergent sequences?
• What is the PAM/Blosum matrix with the highest number?

Additional Slides on blast and databanks (the slides contain links that only become accessible, after you switched to presentation mode)

Discussion 2

E-values and multiple tests

• If you select two sequences from the database and calculate their pairwise alignment score, what would be a useful Null hypothesis to assess the significance.
• How is this null hypothesis implemented in PRSS and FASTA?
• Are the E-value and P-values a measure for false positives or false negatives?
• Assume you have 100 students that repeat this exercise, what should be the expectation for a false positive if the individual test is required to pass the 1% significance level?
• What would you need to do to have false positives with an overall (for all 100 students) rate of 1%? Which significance level would the individual experiment need to pass?

If time:

• Discuss LUCA's properties and the Late Heavy Bombardment (slides)

If more time:

• Go over sequence space slides