Assignment for Friday's class:
- Go through blast slides (class 9 and 10)
- Think about how you will transfer files back and forth from the cluster
Assignment for Monday
- Complete take home exam #3 (due on Monday)
- Bring questions for the review session
Review
- How can one assess the number of false positives in a Blast ?
- How can one assess the number of false negatives in a Blast ?
- Is the E-value of a match independent of the size of the databank?
- If you select two sequences at random and test their significant similarity, what does the E-value signify? Is this the same as the P-value?
Sadly, we have fallen a behind in administering take home exams. We will replace one take home exam with the following:
- Every student writes one entry on the discussion board the provides a blog-like opinion piece on the the ENCODE project (100 words are plenty, 200 words maximum).
- Every student writes at least two comments on the opinion pieces of other students.
To get you into the spirit of things, blog entries and articles on this are here, here, here (here is a video that covers the same ground), and here
Your blogpost-like discussion entry is due on Monday 10/15 and the two responses are due on Wednesday 10/18
On Monday we will have a review session to prepare for the midterm.
Discuss if the concept of phylogeny is compatible with reticulation events. (slides here)
- example of simple perl scripts:
- (perl script to extract top scoring hits is here (pdf)-- extra credit: how would you modify the script, to print out not only the first reported match for a query, but all hits that have equally good E-values to the first one? Note: in Perl the operator for "logical and" is && and "not equal" for a number is != and "not equal" for a string is ne)
- (perl script to replace gi number with position on the genome is here (pdf) (faa_sample, feature_table sample)
- (perl script to make gnuplot is here (pdf), output for Thermotoga maritima vs Th. petrophila is here, plots for comparison between different Aeromonas species are here, here and here). Discuss: Which recombination events could have created these patterns?
What can give rise to recombination events occuring mainly between points that are equidistant to the origin of replication?
- See Collins Tillier
- Strand bias (slides here)
If time:
Goals class 11:
- Understand that the evolution of genomes is best depicted as a network.
- Appreciate that life may be older than the late heavy bombardment.
- Understand the Coral of Life metaphor and the possibility that now extinct lineages have contributed to the gene pool of extant organisms.
- Understand the gen-plot like diagrams, and what they imply for the occurance and fixation of intra chomosomal recombination.
