Remark for those that need to make up the computerlab:

• Filefilla (for file transfer) and PuTTY are available free of charge for the different operating systems.
• Some things are only accessible whe you are at a computer inside the UConn domain (or via vpn).
  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)
  

Slides on M. Dayhoff and the origins of genbank (the slides contain links that only become accessible, after you switched to presentation mode)

Discussions

PAM versus Blosum

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

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 sequencing slides
• sequence space slides