I have two variety, one is A - in vivo plant leaf and B - in vitro plant leaf. i had extracted DNA from these both samples A & B. Done PCR with 31 RAPD primers and got varies band pattern on gel. I have made binomial matrix 0 & 1 foe absent and presence of band respectively. now how can i prepare dendogram for this data?
Dendogram will be made different for all these primers or it can be made single for these all primers data?
From these matrix dendogram will be prepared or should I convert the data in distance matrix or something else?
Please, help me completing my analysis.
Hi! Jigar,
I believe you might have seen the answer given for the earlier question where you have posted gel picture. I told in the beginning first by taking two samples check with all primers select those primers give good number of bands, use them for further data development. Create/develop (0,1) matrix for all primers separately for in vivo, in vitro.
I hardly seen variation for the sample pictures given in the manuscript of Ramakrishna, anyway.
Seems for the pictures that you posted got variation.
By the way may I know a bit about your supervisor/guide?
If you need more information about RAPD-PCRs check patiently my Answer link, I answered many questions in the very beginning.
Good luck!!!
hello mam,(Jetty Ramadevi)
i have told you that i prepared the 0-1 matrix for all the primer aor both in vitro and in vivo, now what should be done next to it.?
Once you generate the matrix you feed that to the software you have chosen to analyze (I told many are available, do you know the names, cite one or two). Make separately for in vivo n in vitro considering all primers you have used. How many primers you have used? at least 10 or 15 or 20. Can I have your matrix for one RAPD primer along with gel picture. Even after telling clearly you are unable to follow.
I asked 'By the way may I know a bit about your supervisor/guide?' so your supervisor will not guide/clear this kind of doubts. Great guidance.
Thank you jetty ramadevi for your precious time and valuable help.
After you get the gel images in RAPD experiments, selecting correct analytic algorithms become the key for the data analysis. Please see my papers in ResearchGate :
Suitability and Advantages of Abundance-Weighted Algorithms for the Holistic Comparison of Sample Systems. J Appl Biotechnol Bioengineering, 2017, 2(6): 00050
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