03511/03711 - Syllabus

Computational Molecular Biology and Genomics - Syllabus, Fall 2022

The materials in the "Assigned Reading" column are directly related to the topics covered in class. Readings under "Additional Topics" are strictly optional and will not be covered on the exams.

In some cases, the same material is covered in more than one textbook. You have the choice of selecting the text that presents a treatment of the material most to your liking. It is your responsibility to make sure that you understand the material covered in class and you may read as many or as few of these texts needed to achieve that goal.

Access to full Lecture Notes Updated Lecture Notes (10/24/22)

CLASS	DATE	TOPICS	ASSIGNED READING	ADDITIONAL TOPICS
1.	Aug. 30	Introduction Pairwise sequence alignment (lecture notes, pp. 1 - 9) PS0 due 10am on Tuesday, Sept. 6th	Review biology and algorithms background
2.	Sep. 1	Global pairwise sequence alignment, class notes pp. 1-9 Alignment examples distance scoring. similarity scoring.	Global pairwise alignment - Setubal and Meidanis, 47-57, 89-92, 96-98; - Durbin, 17-24	Saving space, - Setubal and Meidanis, 58-60; (physical reserve) General and affine gap penalty functions, - Setubal and Meidanis, 60-66 (physical reserve) - Durbin, 29-30 Semi-global alignment - Setubal and Meidanis, 56-57,
3.	Sep. 6	Local pairwise alignment Local alignment examples. PS0 DUE 10am via Canvas	Local pairwise alignment - Setubal and Meidanis, p. 55, - Durbin, 23-24
4.	Sep. 8	Local pairwise sequence alignment. PS1 due midnight Friday, Sept. 16th	Markov Chain background - Ewens and Grant, 4.4-4.8 - Durbin et al., 48-51 (Section 3.1)
5.	Sep. 13	Introduction to Markov chains and random walks (lecture notes, Section 2.1-2.2) 7Eleven assignment 1 due midnight on Wed, Sept.21st
6.	Sep. 15	Markov models of sequence evolution, Jukes-Cantor model (lecture notes, Section 2.3 ) PS2 due midnight Friday, Sept. 23rd	Models of nucleotide substitution - Durbin et al., 8.2, pp. 193 - 197 only
7.	Sep. 20	Markov models of sequence evolution, applications of DNA substitution models (lecture notes, Sections 2.3 and 2.4) Seven11-1 due tomorrow (Wednesday) at midnight
8.	Sep. 22	Applications of DNA substitution models (lecture notes, Section 2.4) Jukes-Cantor worksheet PS3 due midnight Friday, Sep 30.
9.	Sep. 27	Log-odds scoring (lecture notes, Section 3.1)
10.	Sep. 29	Amino acid substitution matrices: PAM matrices (lecture notes, Section 3.2) Today's slides PS4 EXTENSION due midnight SATURDAY Oct 8th.	Substitution matrices: - Setubal and Meidanis, 80-84; - Mount, pp. 76-89; - Durbin et al, pp. 14-16
11.	Oct. 4	Substitution matrices, cont'd PAM250, PAM30 7Eleven-2 due midnight, Fri, Oct 14th
12.	Oct. 6	PAM, PS 4 due SATURDAY Oct 8, at midnight.
13.	Oct. 11	In-class EXAM - This exam is closed book. You may bring two pages (or one page, front and back) of your own notes. - The exam covers material covered in Lectures 1 through 9. Study Guide
14.	Oct. 13	BLOSUM matrices Today's slides BLOSUM62	BLOSUM Matrices: - Ewens and Grant, 6.5.2. - Amino acid substitution matrices from protein blocks, Henikoff S, Henikoff JG., PNAS 89(22):10915-9, 1992
	Oct. 18 & Oct. 20	Mid semester break, NO CLASS.
15.	Oct. 25	Motifs, local multiple sequence alignment, PSSMs, the Gibbs Sampler. PSSM example, with and without pseudocounts. Today's slides PS5 due midnight Oct 30th.	Gibbs sampler Ewens and Grant, 211-215.	Theoretical framework, convergence proofs - Ewens and Grant, 10.5.2, (physical reserves). - Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment, Lawrence et al., Science. 1993 262(5131):208-14. - Explaining the Gibbs sampler, G. Casella & E. I. George, The American Statistician, 46:167-174, 1992
16.	Oct. 27	Gibbs Sampler 7Eleven-34 due midnight, Fri, Nov 11th -->
17.	Nov. 1	Introduction to HMMs
18.	Nov. 3	Introduction to HMMs, cont'd
19.	Nov. 8	HMMs: Recognition Viterbi example, Forward example. PS6 due midnight Fri, Nov 18th	Viterbi, Forward, Backward algorithms - Durbin et al, 55 - 61 - Ewens and Grant, 329-332 .
20.	Nov. 10	HMMs: Modeling, parameter estimation	HMM Topology Durbin et al, 68-71 Parameter estimation, Baum-Welch algorithm Durbin et al, 61-71 Ewens & Grant, 329-332
21.	Nov. 15	HMM topology, Profile HMMs examples	Profile HMMs Durbin et al, 100-110 Multiple alignment using HMMs Ewens & Grant, 335 - 337
22.	Nov. 17	Multiple alignment using Profile HMMs PS7 due midnight Fri, Dec 2nd		Protein multiple sequence alignment, Do and Katoh, 2008. (electronic reserves)
24.	Nov. 22	Profile HMMs Today's slides 7Eleven-5 due midnight, Sun, Dec 4th
	Nov. 24	Thanksgiving Holiday: No class
24.	Nov. 29	Searching sequence databases The Basic Local Alignment Search Tool (Blast).	Blast 1990 - Setubal and Meidanis, 84-87 - Basic local alignment search tool, Altschul et al. , J. Mol. Bio., 1990
25.	Dec. 1	The statistics of database searching PS8 due midnight Fri, Dec 9th	Blast statistics and data base searching: - The statistics of sequence similarity scores S. F. Altschul - Amino acid substitution matrices from an information theoretic perspective, S. F. Altschul, J. Mol. Bio., 219:555-565, 1991 . - A protein alignment scoring system sensitive at all evolutionary distances, S. F. Altschul, J. Mol. Evol., 36:290-300, 1993.
26.	Dec. 6	Blast statistics continued, Today's slides
27.	Dec. 8	Blast statistics continued, Today's slides
Final exam	Dec. 12	Final exam 8:30am - 11:30am Hamerschlag B131 Study Guide	The exam covers the entire semester, but with a strong emphasis on the last third of the course. This exam is closed book. You may bring four pages (or two pages, front and back) of your own notes.

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Last modified: Dec 10, 2022.