http://www.cs.unc.edu/~prins/Classes/555/
Fall 2014
Instructor:
Jan Prins
|
Computational methods are fueling a revolution in the biological sciences. As a result, two new multidisciplinary fields, bioinformatics and computational biology, have emerged. This course will explore the computational methods and algorithmic principles driving this revolution. It will cover basic topics in molecular biology, genetics, and proteomics. The course also addresses basic computational theory and algorithms including asymptotic notation, recursion, divide-and-conquer approaches, graph algorithms, dynamic programming, and greedy algorithms. These fundamental concepts from computer science will be taught within the context of motivating problems drawn from contemporary biology. Example biological topics include sequence alignment, motif finding, gene rearrangement, DNA sequencing, protein peptide sequencing, phylogeny, and gene expression analysis.
Date | Lecture Topic | Reading Assignment | Homework |
August 19 | Introduction | Chapter 1, Chapter 3 Secns 3.1 - 3.7 | |
August 21 | High Throughput Biology | Chapter 3 | |
August 26 | Algorithms and Complexity | Chapter 2 | |
August 28 | Restriction Mappings | Chapter 4 secns 4.1 - 4.3 | Assignment 1 |
September 2 | Finding Regulatory Motifs | Chapter 4 secns 4.4 - 4.9 | |
September 4 | Greedy Algorithms | Chapter 5 secns 5.1 - 5.2 | |
September 9 | Genome Rearrangements | Chapter 5 secns 5.3 - 5.5 | |
September 11 | Dynamic Programming Preliminaries | Chapter 6 secns 6.1 - 6.3 | |
September 16 | Sequence Alignments | Chapter 6 secns 6.4 - 6.8 | Assignment 1 due |
September 18 | Local Sequence Alignment | Chapter 6 secns 6.8 - 6.10 | |
September 23 | Gapped and Multiple Alignment (see addl slides in Lecture 10) |
Chapter 6 secns 6.8 - 6.10 | |
September 25 | Gene Prediction | Chapter 6 secns 6.11 - 6.14 | Assignment 2 |
September 30 | Divide and Conquer Algorithms | Chapter 7 secns 7.1 - 7.4 | |
October 2 | Graph Algorithms | Chapter 8 secns 8.1 - 8.8 | |
October 7 | homework solutions and midterm review | Assignment 2 due | |
October 9 | Midterm Exam Chapters 1 - 7, Lecs 1 - 12 | ||
October 14 | midterm solutions | ||
October 16 | Fall Break (no class) | ||
October 21 | DNA Sequencing and Assembly | Chapter 8 secn 8.9 | Assignment 3 |
October 23 | Protein Sequencing and Identification | Chapter 8 secns 8.10 - 8.15 | |
October 28 | Combinatorial Pattern Matching | Chapter 9 secns 9.1 - 9.5 | |
October 30 | Suffix Arrays and BWT | (not in text) | |
November 4 | Approximate Pattern Matching | Chapter 9 secns 9.6 - 9.8 | Assignment 3 due |
November 6 | Clustering | Chapter 10 secns 10.1 - 10.3 | |
November 11 | Clustering and Evolution | Chapter 10 secns 10.4 - 10.8 | Assignment 4 due Nov 25 |
November 13 | Imperfect Tree Construction | Chapter 10 secns 10.9 - 10.11 | |
November 18 | Hidden Markov Models | Chapter 11 secns 11.1 - 11.3 | |
November 20 | Randomized Algorithms | Chapter 12 | |
November 25 | Complete material from last class | Chapter 12 | Assignment 4 due Assignment 5 due Wed Dec 3 |
December 2 | Special topic on RNA-seq alignment techniques | (no reading) |
import pickleat the head of your program, and use the following code in your program
datafile = open("cdata.txt","r") vals = pickle.load(datafile)Prepend a path to the filename if the file is not in python's working directory.
scp path-to-your-file-hw4.py yourlogin@classroom.cs.unc.edu:/afs/unc/project/courses/comp555/Submit/yourlogin/hw4you will be prompted for your cs passwd to complete the transfer.
/afs/unc/project/courses/comp555/Submit/yourlogin/hw4Locate your file hw4.py on your machine in the sftp window and drag it to the remote side.