The basic concept (in my opinion): All of the instructions needed to create an organism are encoded in its DNA. Thus, one should be able to predict all of an organism’s characteristics from knowledge of its DNA sequence alone. We are a long way from being able to do this! It requires a lot of experimental data to accomplish this: there are a lot of steps between the DNA sequence and the organism’s phenotype. on the other hand, DNA sequencing is cheap and easy, while lab work is slow and expensive. Thus many organisms with completely sequenced genomes will have only minimal lab work performed on them. Bioinformatics will be needed to fill in the gaps.
Bioinformatics is the application of computers, databases, and computational techniques to the study of biological information, primarily in molecular biology.
Meeting time Class is scheduled for MW 1-2:50, in MO 443. However, we will start at 1:15 and go to 2:30.
Office hours: MWF 9-11 or by appointment. Or just drop by, but realize that I may be busy. MO 409.
Email is the best way to contact me (rjohns@niu.edu). I am usually at my desk and the e-mail is always on. I am not too fond of telephones and almost never return calls. Given all that, if you really need to call me, my number is 753-7836.
Subject Matter. We are going to cover 5 main areas:
| Introduction: Biological Background | 3 week | Chapters 1, 2, 3 |
| Sequence alignment | 3 weeks | Chapters 4, 5, 6 |
| Phylogenetic analysis | 2 weeks | Chapters 7, 8 |
| Genomics | 3 weeks | Chapters 9, 10 |
| Gene expression data | 2 weeks | Chapters 15, 16 |
| Protein structure | 2 weeks | Chapters 11, 12, 13, 14 |
My lecture notes will be posted below, as PowerPoint slides. I will be actively revising the notes during the semester, so please don't get too far ahead of me in printing these out.
| Smith-Waterman and BLAST assignment |
They open in new tabs.
| KEGG Home page and table of contents |
| Metacyc Biochemical pathways, an alternative to KEGG |
| UniProt |
| SEED Viewer It doesn't require you to login. |
| Protein Data Bank (PDB) Structural Information about proteins |
| NCBI Home page |