Class 4: Analyzing Genomes

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 19 is a bit different, but may be useful to give you ideas for the kinds of things you could do for the Final Project.)
• Read Chapter 5 of the Bioinformatics Algorithms: How do we compare biological sequences?.

Slides

The slides from 31 January class are here: class4.pdf

Some links to materials for the class:

• Richard W. Hamming, Mathematics on a Distant Planet, The American Mathematical Monthly, 1998.

• Nextstrain: Genomic epidemiology of novel coronavirus

• NCBI: Variation in ATP8 Gene

• NCBI Basic Local Alignment Search Tool (BLAST)

• Hovav Shacham. The Geometry of Innocent Flesh on the Bone: Return-into-libc without Function Calls (on the x86). ACM CCS 2007.

• 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.

• Robert A. Wagner and Michael J. Fischer. The String-to-String Correction Problem. Journal of the Association of Computing Machinery, January 1974.