Project 2
Project 2 is now posted, and is due on Wednesday, 21 September, 8:59pm.
Correction to Alignment Code! As was noticed in class today, the code for the gap-based alignment algorithms is wrong. The loops should include all values up to and including j (so should be
range(1, j + 1)
instead of
range(1, j)
(note that range in Python iterates through the values from the first input up to, but not including, the second input value, so to include j in the iteration, we need to use j + 1 in the range).
Thanks to Diego Wang for submitting this pull request with the fix and explanation.
If you have already modified your Project 2 notebook (which hopefully is true for everyone!), you should incorporate the change manually into the code in your notebook to avoid losing the work you have done.
Readings
See Class 5 for this week’s readings.
Slides
The slides are here: Class 7: Estimating Evolutionary Distance
Some links to materials for the class:
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Steven Henikoff and Jorja Henikoff. Amino acid substitution matrices from protein blocks. Proceedings of the National Academy of Science, November 1992. This is the paper that introduced BLOSUM.
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Mark P Styczynski, Kyle L Jensen, Isidore Rigoutsos, and Gregory Stephanopoulos/ BLOSUM62 miscalculations improve search performance. Nature Biotechnology, 2008.
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T. F. Smith and M. S. Waterman. Identification of common molecular subsequences. Journal of Molecular Biology, 1981. Michael Waterman’s UVA Webpage