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University of Toronto St. George
John Coleman

Bioinformatics Part 1: A short history of bioinformatics  DNA sequencing: precise order of nucleotides  Human Genome project is used to sequence all genes in an organism  Now many organisms can be sequenced  Ex. Genbank is a public repository of DNA Nucleotide Sequence Databases  Genbank has all publicly available nucleotide and protein sequence Part 2: Database Analysis Tool BLAST  Used as a comparative analysis  You can line up two sequences to determine the similarities  The BLAST program: Basic Local Alignment Search Tool is a database that can be used to compare DNA  BLAST is the “one-against-all” CLUSTALW  It can determine which sequence is the most similar to the sequence  This is also called the multiple sequence Alignment  CLUSTALW is “many-against-each-other” ENTREZ  Interfaces with several databases Why use BLAST?  Determine “conserved” region remain the same for periods of time  Determine “variable” region changes BLAST similarity Score and Statistical Significance  Similarity is a quantified or a measure of a BLAST score  Homologous is common evolutionary history  Lower E value the more closely related the another species  P=1-e^(-E)  E-value and P-value should be 0.01 to be significant Cell & Microscopy Introduction  Microcopy is observing the cell structure and cellular mechanisms  Need to learn how to determine the Koehler illumination Procedure Part 1 Protocol-Adjusting your microscope for Koehler illumination  Koehler illumination allows bright and even illumination across a specimen  It will maximize the resolution Set-up  1. Begin with x10 objective and turn the microscope on  2. Test the distance between the ocular lens  Adjust the focus adjustment knob Adjustment for Koehler illumination  1. Open the field iris diaphragm and condenser
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