I did RAPD method of one sample. I used 10 primer for that. now I have one image of that result, how can I calculate and interpret result using polymorphism phylogenetic mapping? is there any software?
@Madhavi Hardik Patel
You may check my paper for the methods of RAPD polymorphism analysis.
Ni LQ, Yao Y-S, Gao L, Wu Z-M, Tan NZ, Zhu JS. Arithmetic methods for similarity computation and cluster tree construction in RAPD analysis on a multi-fungi microecology system, Cordyceps sinensis. Am J BioMed Sci, 2014, 6(2): 82-104
@Vivek Vaishnav
You provided a beautiful art work. Although the density-unweighted algorithms that you aforementioned have been wildly recogniced and used in population genetic studies, these algorithms may not be suitable in many cases of RAPD studies. There are two specific computational biology prerequisites for use of the density-unweighted algorithms in the studies such as RAPD: (a) all matched DNA pairs in the electrophoretic lanes being compared must have essentially the same densities, as illustrated in the book provided; and (b) all DNA amplicons must be well separated from the adjacent DNA moieties with similar molecular weights and conformations by electrophoresis.
Ni et al. 2014 (Am J BioMed Sci, 2014, 6(2): 82-104) devolupped the density-weighted algoritms, which is mathematically general with no specific prerequisites and governs all conditions, in contrast to the density-unweighted algorithms that narrow the specific cases under the strict prerequisites (a) and (b) described above.
Best,
Josh
Dear Madhavi Hardik Patel
Greetings, thank you for your question.
It depends in your project i.e., genetic diversity or mapping.
Also, it depends on the program.
So, I hope send a picture or the objective of your study
waiting your kindly reply
khaled
@Khaled F M Salem
Yes, Khaled. You are right. It depends. If Madhavi's data meets the computational biology prerequisites for use of the density-unweighted algorithms, she may use those algorithms for data analysis. If, on the other hand, the data does not meet the prerequisites, the density-weighted algorithms are the option of choice. However, as I mentioned, the density-weighted algoritms are mathematically general with no specific prerequisites and governs all conditions, including the cases under the strict prerequisites.
Best,
Josh
Please see:
https://helda.helsinki.fi/bitstream/handle/10138/42438/PICcalc_2012_BIGI.pdf?sequence=2
http://www.imedpub.com/articles/random-amplified-polymorphic-dna-rapd-analysis-for-genetic-diversity-in-terminalia-bellirica-species-roxb-an-important-medicinal-t.pdf
http://homepages.uc.edu/~culleyt/Population%20Genetic%20Analysis%20of%20ISSR%20Data.pdf
thank you for your kind suggestion.
Here I am attaching the file for which I want to conclude result. I don't know how to give result in effective way or suggest me further.
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