Assignment for Friday's class:

• Go through today's blast slides and think about how you will transfer files back and forth from the cluster.

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 an alternative explanation?

Discussion

PAM versus Blosum

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

Powerpoint slides on

• blast and commandline blast (the slides cotain links that only become accessible, after you switched to presentation mode)
• sequence space