Bioinformatics Home

Comparative Bioinformatics -- BSCI 380
Syllabus Fall 2006 (with Tentative Lecture Schedule)

Optional reviews of molecular biology and UNIX may be offered during the semester.

Date Lecture Topic Pevsner Reading
W Aug. 30 Introduction Chapters 1 & 2


1 Whole genome analysis, Randomness  
M   4 Labor Day (Holiday)  
Understanding and Navigating Sequence Databases, Pairwise Alignment Tools
W   6 Case Study: The genomes of bacterial pathogens Chapter 3
F   8 Sequence Databases  
M   11 Point mutation and Amino acid substitution matrices, Models  
W   13 Pairwise sequence alignment  
F   15 Contemporary Research: Borrelia burgdorferi  
M   18 Pairwise sequence alignment (cont.) Chapter 4
W   20 BLAST, FASTA and Other Heuristic Alignment Tools  
F   22 BLAST (cont.)  
M   25 Assessing alignment significance Chapter 5
W   27 Hidden Markov Models  
F   29    
Working with Genomic Data
M   2 Strategies for sequencing complete genomes & sequencing technologies Chapter 12
W Oct. 4 Contemporary Research  
F   6 Midterm exam  
M   9 Contig Assembly (Chaps. 13-17)
W   11 Determining the number of genes, gene finding  
F   13 Contemporary research: Deinococcus radiodurans  
M   16 Genomes (cont.)  
W   18 Domains of Life Chapter 8
F   20 EST Analysis (Guest Lecture)  
M   23 Gene families  
W   25 Genome organization Chapter 6
F   27 Contemporary Research: Comparing Yeast Genomes,  

Using Comparative Methods

M   30 Multiple sequence alignment  
W Nov. 1 Phylogenetic analysis:Parsimony methods Chapter 10
F   3 Horizontal Gene Transfer and an example from rubisco  
M   6 Models of Nucleotide Sequence Evolution  
W   8 Model based phylogenetic methods 1: Distance Chapter 11
F   10 Distance methods (cont.)  
M   13 Model based phylogenetic methods 2: Likelihood  
W   15 Likelihood (cont.)  
F   17 Contemporary Research  
M   20 Gene families revisited  
W   22 Midterm exam  
F   24 Holiday - Thanksgiving break  
M   27 RNA-coding genes; finding & predicting secondary structure  
W   29 Contemporary research Chapter 7
F Dec 1 Human X & Y chromosomes  
M   4 Gene finding & genome annotation (El-Sayed; Powerpoint File)  
W   6 Inferring function (El-Sayed; Powerpoint File)  
F   8 Contemporary Research  
M   11 Future prospects for bioinformatics  
Sa Dec. 16 8:00 am - 10:00 am Final Exam 1229 HJ Patterson Hall  

Laboratory & Computer Practicum

Week Lab Topic Notes
  Sep 4 No lab  
    11 Introduction and Working with BLAST (click here for an old version)  
    18 More on the NCBI web site (old version)  
    25 Intro unix, local tools, remote tools, host and client (old version) Homework
  Oct 2 More UNIX, putting tools you already know into use. BLAST revisited; 3
    9 Basic tools and file manipulation -- Cnidarian exercise  
    16 Analysis of an unknown sequence; PSI-Blast and other tools 5
    23 Contig assembly 6
    30 Lab is not in Plant Sciences! Do this exercise on online resources at home. 7
  Nov 6 Multiple Sequence Alignment 8
    13 Phylogenetic methods 1 (Phylip) 9
    20 Phylogenetic methods 2 10
    27 Lab is not in Plant Sciences! The assignment is here, and will continue next week. 11
  Dec 4 Project 12
    11 No Lab  

Bonus Topics

      Genome Exploration: the cDNA approach  
      Determining the number of genes