03511/03711 - Syllabus

Computational Molecular Biology and Genomics - Syllabus, Fall 2025

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 Lecture Notes

CLASS	DATE	TOPICS	ASSIGNED READING	ADDITIONAL TOPICS
1.	Aug. 26	Introduction Pairwise sequence alignment ( lecture notes , pp. 1 - 3)	Review biology and algorithms background
2.	Aug. 28	Readyness Quiz
3.	Sep. 2	Global pairwise sequence alignment ( lecture notes , Section 1.1) Global alignment examples similarity scoring. distance 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 ,
4.	Sep. 4	Local pairwise alignment ( lecture notes , Section 1.2) Local alignment examples.	Local pairwise alignment - Setubal and Meidanis, p. 55 , - Durbin, 23-24
5.	Sep. 9	Global multiple sequence alignment ( lecture notes , Sections 2.1, 2.2)	Global multiple alignment using dynamic programming - Setubal and Meidanis, pp. 69-72, 79-80. - Durbin, 6.1 -- 6.3
6.	Sep. 11	Global multiple alignment: heuristic methods Today's slides Lecture notes , Sections 2.3	Global multiple alignment: heuristic methods - Durbin, 6.4	Protein multiple sequence alignment, Do and Katoh, 2008. A survey on the algorithm and development of multiple sequence alignment, Zhang et al, 2022.
7.	Sep. 16	Introduction to Markov chains. Lecture Notes Sections 3.1	Markov Chain background - Ewens and Grant, 4.4-4.8 - Durbin et al. , 48-51 (Section 3.1)
8.	Sep. 18	Markov chains, Lecture Notes Sections 3.1 Problem set 2, due Fri, 9/26, at 11:59pm.
9.	Sep. 23	Markov models of sequence evolution Lecture Notes Section 3.2 Today's slides Periodicity handout	Models of nucleotide substitution - Durbin et al. , 8.2, pp. 193 - 197 only
10.	Sep. 25	Applications of DNA substitution models Lecture Notes Section 3.3 Today's slides Problem set 2, due tomorrow at midnight.
11.	Sep. 30	Applications of DNA substitution models: Correcting for multiple substitutions. Lecture Notes Section 3.3.3 Log odds scoring Lecture Notes Section 4.1 Today's slides EXAM 1: 7:30pm - 9:30pm, DH 5403 - 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.
12.	Oct. 2	Phylogenetics
13.	Oct. 7	Amino acid substitution matrices Log odds scoring Lecture Notes Section 4.1 Today's slides
14.	Oct. 9	Amino acid substitution matrices PAM matrices Lecture Notes Section 4.2 PAM30 , PAM250 Problem Set 3, due Friday October 24th. pdf, latex zip file	Substitution matrices: - Setubal and Meidanis, 80-84; - Mount, pp. 76-89; - Durbin et al, pp. 14-16
	Oct. 14 & Oct. 16	Mid semester break, NO CLASS.
15.	Oct. 21	Amino acid substitution matrices PAM matrices (review) Lecture Notes Section 4.2 BLOSUM matrices Lecture Notes Section 4.3 BLOSUM62 Today's slides /	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
16.	Oct. 23	Searching sequence databases The Basic Local Alignment Search Tool (Blast). Lecture notes, section 5.1 Mid-semester scores Problem set 3, due tomorrow at midnight.	Blast 1990 - Setubal and Meidanis, 84-87 - Basic local alignment search tool, Altschul et al. , J. Mol. Bio., 1990 - Gapped BLAST Altschul et al. , Nucl. Acids Res.., 1997
17.	Oct. 28	Blast Statistics Today's slides	Blast statistics and data base searching: - The statistics of sequence similarity scores S. F. Altschul
18.	Oct. 30	The statistics of database searching Information content of substitution matrices Information content of alignments Today's slides	Blast statistics and data base searching: - 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.
	Nov. 4	Election Day; No class
19.	Nov. 6	Statistics of database searching, cont'd Today's slides
20.	Nov. 11	Blast demos Exam 2: 7:30pm - 9:30pm WH 5403
21.	Nov. 13	Motifs, local multiple sequence alignment Position Specific Scoring Matrices (PSSMs) Lecture notes, section 6.1 PSSM examples pseudocount: b=1 pseudocount: b=0.1 Today's slides		Gibbs sampler Ewens and Grant, 211-215 .
22.	Nov. 18	Hidden Markov models (HMMs) for sequence analysis Introduction Lecture Notes 7.1-7.3 Today's slides Forward example	Parameter estimation with labeled sequences: Lecture Notes 7.6.2, pp. 146-148.	Tutorial on Hidden Markov Models, L.R. Rabiner, Proc. IEEE, 1989
23.	Nov. 20	HMM recognition algorithms Lecture notes, section 7.4, 7.5 Viterbi example
24.	Nov. 25	HMM recognition, discovery Lecture notes, section 7.4, 7.5, 7.6.2 Today's slides	Parameter estimation, Baum-Welch algorithm Durbin et al, 61-71 Ewens & Grant, 329-332
	Nov. 27	Thanksgiving Holiday: No class
25.	Dec. 2	HMM design Profile HMMs Today's slides	HMM Design - Durbin et al, Section 3.4, HMM model structure 68 - 71 Profile HMMs Durbin et al, 100-110
26.	Dec. 4	Multiple sequence alignment with profile HMMs Today's slides	Multiple alignment using HMMs Ewens & Grant, 335 - 339
Final exam	Dec. 12	Final exam WEH 5403 5:30pm- 8:30pm	The exam covers the entire semester, but with a strong emphasis on the last third of the course: Study Guide This exam is closed book. You may bring four pages (or two pages, front and back) of your own notes. You will not need a calculator.

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Last modified: Dec. 4, 2025.