Synteny: Getting the Big Picture

Background Information

Objective:  To have you learn about Syntenic Dotplots while generating one.

Difficulty:  Easy

Estimated Time:  5 minutes

New Programs Used:  SynMap

Lesson

Introduction

     The image to the right is a syntenic dotplot.  This lesson teaches you what a syntenic dotplot is, how it is used, and why it is useful.  You will also learn how to create a syntenic dotplot through SynMap.

Syntenic Dotplots

• Syntenic dotplots compare two genomes to each other
• In the picture to the right the green dots show homologous regions, regions where there are similar genes between two organisms
• The x-axis represents one organism's genome and the y-axis represents the other organism's genome
• Each box within the graph represents one chromosome
  
• See more detailed information

Procedure

     1.  Open Synmap (quicklink) and search for human in the Organism 1 Search box.  Select Homo sapien (the first result)

     2.  Search for chimp in the Organism 2 Search box.  Select Pan troglodytes (chimpanzee)

     3.  Click Generate SynMap

          -  Note:  Very powerful computers need to compare the genomes against one another, and remember that each genome is over 3 billion basepairs long.  Luckily once two organisms have been compared to eachother the computers save the result so that the next person to compare the same organisms does not have to wait.  It takes hours for Synmap to generate a syntenic dotplot for humans and chimpanzees the first time.

     4.  The new window that pops up is your syntenic dotplot.  Move your cursor to a point over any green section, your cursor should turn red.  Click this section

     5.  The GEvo window should pop up now with all the information filled out for that section.  (you are preparing to take a close up look at the section you clicked on)

     6.  Click Run GEvo Analysis!

See Also

Previous Lecture:  Computationally Comparing Different Genomes

Next Lecture: 

All Lectures:  Tutorial for High School Students