TO SCORE RAPD's - (Sep/29/2001 )
I'am a marine biologist student of the Autonomous University of Baja California SurMéxico. I'm starting my thesis on genetic variability of B.C.S. sea turtles. As my porpuse I'm planing on using the RAPD's markers; the problem is I don't Know how to score or read my results and that's the reason for writting you hoping you would take a piece of your valuable time to explain me.Any help would be greatly appreciatedSincerely thankfulHector.
RAPDs, as you know are dominant markers which make use of random primers to find out polymorphism at DNA level. When you amplify fragments identified by the primer in use and then separate them on Agarose gel, they form a banding pattern according to their size and molecular weight. You score them by counting the presence of band as 1 and absence as 0 and generate a matrix which you can feed to some statistical packages to analyse and interpret the variability. I know some programmes which you might use for the analysis. POPGEN () is one of them. You can find a list at http://fisher.genfys.slu.se/pgen/software.htm. More detailed lists could be found out by using "population genetics software" search syntax in any search engine.
Like you, I am too a student and have used RAPDs to an extent so I might not be very clear in my answer. If you want we can discuss this more.
Best luck for your studies.