INTD 388: Bioinformatics


Brad Goodner

Office: Colton 222 Research Lab: Colton 115, Phone: x5260, Email:

Ellen L. Walker

Office: Colton 112 Colton, Phone: x5250, Email:

Administrative Links


Class Schedule

DateTopicText Readings
T 1/8Course Intro, Biological Problems in Need of Solutions
R 1/10Algorithms as Possible SolutionsA Chapter 2
T 1/15 Algorithmic Techniques and Biological Strings (DNA Replication, Transcription)B 19-22 (Begining of Chapter 2 up to section "Protein"), or A Chapter 3
R 1/17Biological Strings (Translation); Problem Solving; Intro to Perl B 22-27 (Chapter 2 "Protein" up to "Mutation"), 35-37 (Chapter 2 "Genomes and Genes" up to "Pseudogenes"); P Chapter 3
T 1/22Regular Expressions and Patterns in Biology; Problem Solving A 83-91, P Chapter 4
R 1/24No Class
T 1/29Regular expressions in Biology and Computer ScienceP Chapter 4
R 1/31Practice with Regular Expressions
T 2/5Exam I
R 2/7Perl: Subroutines and FilesP Chapters 7 and 8
T 2/12Global vs. Local Sequence AlignmentsB 3 (What is Blast?), 32-33 (Homology, Phylogeny & Trees and The Tree of Life), 40-53 (All of Chapter 3)
R 2/14Dynamic Computation Algorithms (example perl files) and BlastA Chapter 6, sections 6.1, 6.2, 6.4, 6.6, 6.8
T 2/19Alignment Algorithms, including BLAST + Worksheet B Chapter 5, also A chapter 9 especially 9.6-9.8
R 2/21How BLAST Works (continued) B Chapter 6, Chapter 7 through "The Expect of an HSP"
T 2/26Ab Initio Gene CallingA 197-200 (6.12) GLIMMER Paper, A Chapter 11 (Background on Hidden Markov Models and the decoding problem)
R 2/28Project 1 Presentations
T 3/4Project 1 Presentations
T 3/18Exam II
T 3/18Research for Project 2
T 3/25Beyond BLAST analysis of protein sequences Predicting protein function from sequence and structural data
R 3/27Introduction to Databases
T 4/1Hidden Markov Models A Chapter 11
R 4/3Work on Project 2
T 4/8Project 2 Presentations
R 4/10Exam IIIStudy Guide

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