PBGG/CRSS/PBIO/HORT 8871: Genome Analysis and Comparative Genomics
Introduction:
This 1-credit hour course introduces graduate students to the methodologies used in genetic mapping, genome analyses and comparative genomics. The material is presented as formal lectures and is enhanced by hands-on mapping exercises. You will learn how to construct a genetic map, conduct comparative analysis at the map and DNA sequence level, and become conversant with the cutting-edge technologies that exist in genome analysis. Some key papers related to markers/genetic mapping will be discussed.
All academic work must meet the standards contained in ‘A Culture of Honesty’. Students are responsible for informing themselves about those standards before performing any academic work. The link to more detailed information about academic honesty can be found at: http://www.uga.edu/ovpi/honesty/acadhon.htm.
Instructor:
Katrien M. Devos
Office: Miller Plant Sciences Bldg. Rm. 4107
Phone: 542-0925
Email:
Office hours:
Drop-in’s will be accommodated whenever possible, but better to make an appointment.
Miscellaneous:
When: Spring 2016, Weeks 6-10.
Class times: Tuesdays and Thursdays from 12.30 pm – 1.45 pm
Where: Davison Life Sciences Bldg., Rm B118
Grading:
A-F
50% on class/home work (includes final Jeopardy quiz)
50% on final exam (take-home)
Tentative schedule
Tue 16th February: Markers: Lecture
Thu 18th February: Markers (cont.): Lecture
Tue 23rd February: Mapping: Lecture
Thu 25th February: Practical exercise: using Mapmaker to construct a linkage map
Tue 1st March: Practical exercise: using Mapmaker to construct a linkage map
Thu 3rd March: Map-based cloning: Lecture
Tue 8th March: Spring break
Thu 10th March: Spring break
Tue 15th March: Map-based cloning: Lecture
Thu 17th March: Comparative genomics: Lecture
Tue 22nd March: Discussion of mapping issues /paper
Thu 24th March: Jeopardy – Questions related to the course
For Mapmaker practice:
Please download Mapmaker from:
http://www.plantbio.uga.edu/~russell/index.php?s=1&n=5&r=0
The information given in class pertains to the PC version of Mapmaker.
There is no Mapmaker version available for Macs. Please bring your lap tops with Mapmaker installed to class.
Mapmaker is a DOS program, and to facilitate things, you will want to run commands in batch. In order to do so, you will need to do the following (this is for windows 7; I assume it will be similar for Windows 8 and 10):
Go to Control Panel
Click on 'System'
Click on 'Advanced system settings'
Click on 'Environment variables'
Highlight 'PATH' and click on 'edit'
Copy the path to notepad and save in case you accidentally delete something in the path.
Add c:\mapmaker\ at the end of the path, separated from the last entry by ; (that's assuming that you installed mapmaker in the c:\mapmaker\ subdirectory. Otherwise add the path to wherever you installed mapmaker).
Restart your computer.