Schedule and Readings
Due Tuesday, 8 February (4:59pm): Project 1
Before Wednesday, 9 February:
- Read Chapter 19 – 26 of Hubert’s The DNA Book. (Chapter 26 on Mutations and Changes is the one most relevant to today’s class.)
- Read Chapter 5 of the Bioinformatics Algorithms: How do we compare biological sequences?.
Slides
The slides from 2 February class are here: class5.pdf
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.