Project 2
Project 2 is now posted, and is due on Wednesday, 21 September, 8:59pm.
Office Hours Update
The location for Ashley’s office hours has moved to Olsson Hall 204. Other than the location, the office hours schedule is unchanged:
Monday, 11am-noon: Jack (Rice 414)
Monday, 1:30-2:45pm: Dave (Rice 507)
Wednesday, noon-1pm: Ashley (Olsson 204)
Wednesday, 2-3pm: Jack (Rice 414)
Friday, 11:30am-12:30pm: Ashley (Olsson 204)
Readings
(Repeated from Class 5)
Before Thursday, 8 September:
- Read Chapter 5 of the Bioinformatics Algorithms: How do we compare biological sequences?.
Before next Tuesday, 13 September:
- Read Chapter 19 – 27 of Hubert’s The DNA Book. (Chapter 20 is a bit different, but may be useful to give you ideas for the kinds of things you could do for the Final Project.)
Before next Thursday, 15 September:
- Chapter 26 of Manolis Kellis et al., Computational Biology - Genomes, Networks, and Evolution: Molecular Evolution and Phylogenetics (also available as [PDF]) (if you prefer to watch a video lecture that this chapter is based on, you can watch MIT CompBio Lecture 19 - Phylogenetics).
Slides
The slides are here: Class 6: Alignment Algorithms.
Some links to materials for the class:
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Saul B. Needleman and Christian D. Wunsch. A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins. Journal of Molecular Biology, 1970.
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Motoo Kimura. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 1980.
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William Pearson. Rapid and Sensitive Sequence Comparison with FASTP and FASTA, Methods in Enzymology, 1990. (Includes the PAM 250 scoring matrix.)
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Gely P. Basharin, Amy N. Langville. and Valeriy A. Naumov. The life and work of A.A. Markov. Linear Algebra and its Applications, 2004.