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Saint Louis University

Computer Science 1020
Introduction to Computer Science: Bioinformatics

Michael Goldwasser

Spring 2019

Computer Science Department


Please note that the schedule for future classes is tentative.

Also note: For each lecture, we denote both a topic as well as the associated reading in the textbook. The live link on the 'topic' leads to a page of my personal notes for that lecture. Those personal notes are not nearly as complete or polished as the associated readings from the text. In truth, they exist mostly to provide a brief outline of the day's lecture. Students are expected to read the associated sections of the text. In cases where my notes include material which is not explicitly in the text, I will add the word "notes" to the explicit reading list.

Week Day Topic Reading Due
Jan 14-Jan 18 Mon Welcome.
Hands-on: sequence assembly
Wed Central Dogma slides
my notes
Pages 16-19 and 37-38 of text
Fri Online Tools/Data Sets
Chapter 1 project (pages 10-15)
Jan 21-Jan 25 Mon No Class: Martin Luther King Jr Day
Wed Begin lab02 (due following Monday) Chapter 2 lab01
Fri Introduction to Python my notes
Jan 28-Feb 1 Mon Python Strings my notes, official documentation lab02
Wed In-class Lab: lab03
Python strings
Fri For Loops, Conditionals my notes hw01
Feb 4-Feb 8 Mon In-class Lab: lab04
Control structures
Wed Continuation of lab04; possible work on hw02 lab04
Fri Pairwise Sequence Alignment (Introduction) Beginning of Ch. 3 hw02
Feb 11-Feb 15 Mon Needleman-Wunsch Algorithm my notes
Exercise: reconstruction
Wed Needleman-Wunsch Algorithm (continued)
Examples with non-trivial score function
Python implementation
Source code: pdf
Fri Lab: Global Sequence Alignments lab05
Feb 18-Feb 22 Mon Intro to hw04 (Smith-Waterman algorithm)
Intro to BLAST (Basic Local Alignment Search Tools)
Chapter 4 hw03
Wed Hands-on introduction to BLAST handout (local copy), video
Fri Lab: BLAST Algorithms lab06
Feb 25-Mar 1 Mon Intro to Phylogenetics
Tree representations
my notes
exercises (solutions)
Wed Recursive algorithms
Tree processing
my notes
Fri First Exam
Mar 4-Mar 8 Mon Tree visualizations with cladograms
Hands-on: lab07
skim Chapter 6 lab07
Wed Chronograms
Hands-on: lab08
Fri Circular chronograms
Hands-on: lab09
Mar 11-Mar 15 Mon No Class: Spring Break
Mar 18-Mar 22 Mon Phylogentic distance metrics
Hands-on Activity -- define distance metric
Chapter 6
my notes
Wed Hands-on Activity -- tree building
(model distance matrix)
(groups' resulting trees)
Fri Tree building algorithms Chapter 7
my notes
Mar 25-Mar 29 Mon UPGMA algorithm pp. 128-129
my notes
Wed Overview of hw06 hw05
Fri Neighbor-Joining Method pp. 137-142
Apr 1-Apr 5 Mon Intro to Assembly Sequencing
Preview of lab10
Chapter 8
Wed Hands-on: lab10 lab10
Fri Second Exam - info
Apr 8-Apr 12 Mon Assembly Algorithm:
Overlap/Layout/Consensus (OLC)
OLC notes (ignore suffix trees)
Wed Assembly Algorithm:
De Bruijn graph assembly (DBG)
DBG notes
Fri Gene Prediction
Open Reading Frames (ORFs)
Apr 15-Apr 19 Mon Shine-Dalgarno Sequences
Wed Sorting by Reversals (Dr. David Letscher) notes
Fri No Class: Easter Break
Apr 22-Apr 26 Mon
Wed Sorting by Reversals (Dr. David Letscher)
Fri lab13: Sorting by Reversals
Apr 29-May 3 Mon lab13: Sorting by Reversals lab13
Wed RNA secondary structure prediction Ch. 12
Fri RNA secondary structure prediction
Nussinov-Jacobson algorithm
Ch. 12
Source code (algorithm, full code)
Example tables (gap=2)
May 6 Mon

May 13 Mon Final Exam (8:00-9:50am)

Michael Goldwasser
CSCI 1020, Spring 2019
Last modified: Thursday, 02 May 2019
Course Home | Assignments | Data Sets/Tools | Python | Schedule | Git Submission | Tutoring