Computationally Comparing Different Genomes

Background Information

Objective:  To have the user compare two very similar organisms to familiarize themself with CoGe while also learning about evolution and ancestry.

Difficulty:  Easy

Estimated Time:  10 minutes

Lesson

Introduction

     A human genome contains over 3 billion base pairs.  Now, if a scientist wants to identify similar portions of DNA in a human genome to a chimpanzee genome, which is also over 3 billion base pairs long, the scientist would need to use a computer program.  This is where CoGe comes in.  CoGe can be used to quickly take a section of a 3 billion base pair genome and find where that section closely matches another genome.  As you finish this lesson you will not only begin to understand how genetics may be used to determine ancestry but also understand how scientists can estimate the when separate species shared a common ancestor.

Part 1 - Finding the DNA sequence of the gene you want to compare

     1.  Open OrganismView (quicklink) and search for the animal you want to have compared and select it, for now use chimpanzee

     2.  Click "Launch Genome Viewer" in the bottom left corner to open a new window that visually depicts the genome

     3.  Click the gene you want to have compared, for now select a random gene.  A small window titled features should pop up containing information on this gene

     4.  Click on the link to the right of "Location:" in the Features window to open a new window that contains the DNA sequence of the gene

     5.  Click "CoGe Blast" to open a new webpage and to begin the blasting process

Part 2 - Blasting the gene to another genome

     1.  You should now be looking at a webpage titled CoGeBlast.  The large box containing many A's, T's, C's, G's and N's shows the DNA sequence for the gene you previously selected.  Now you need to find the entire genome of the other orgainsm you want to compare this gene with.  To do this, search for the organism you want to compare your gene with in the "Organism Name" search box and select it, for now search for human.

     2.  Now that the organism you want to compare is selected (human) click the "+ Add" button to the right of the search results screen

          - Note: If you want to compare youre gene to more than one organism you can repeat steps 1 and 2 of Part 2.