Comparative Bioinformatics -- BSCI
380
Syllabus Fall 2006 (with Tentative Lecture Schedule)
|
Comparative Bioinformatics -- BSCI
380 |
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 |
| F | Sep. |
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 |
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| 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 | |
| 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 | |||
| Microarrays | ||||
| Genome Exploration: the cDNA approach | ||||
| Determining the number of genes | ||||
| dotplot | ||||