Saint Louis University |
Computer Science 1020
|
Computer Science Department |
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 |
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| Wed | Central Dogma |
slides
my notes Pages 16-19 and 37-38 of text |
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| Fri |
Online Tools/Data Sets
lab01 |
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 |
lab03 | ||
| Fri | For Loops, Conditionals | my notes | hw01 | |
| Feb 4-Feb 8 | Mon |
In-class Lab: lab04
Control structures |
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| 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) |
hw04 |
| 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 |
lab08 | ||
| Fri |
Circular chronograms
Hands-on: lab09 |
lab09 | ||
| Mar 11-Mar 15 | Mon | No Class: Spring Break | ||
| Wed | ||||
| Fri | ||||
| 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) |
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| Fri | Tree building algorithms |
Chapter 7
my notes |
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| 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
hw06 |
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| 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) lab11 |
lab11 | ||
| Apr 15-Apr 19 | Mon |
Shine-Dalgarno Sequences
lab12 |
hw07
lab12 |
|
| 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
examples |
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| Fri |
RNA secondary structure prediction
Nussinov-Jacobson algorithm |
Ch. 12
Source code (algorithm, full code) Example tables (gap=2) |
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| May 6 | Mon | |||
| May 13 | Mon | Final Exam (8:00-9:50am) | ||