Suppose I have scored 6 allele for an SSR marker in 50 population with major allele frequency of 0.2448. Now how can I determine the required PIC for the marker?
with this formula:
(PIC = 1-∑ (Pi)2, where Pi is the proportion of samples carrying the ith allele of a particular locus)
Thank you Hamed, Actually I am totally new to this field. Hamed how I can calculate the gene diversity from allele frequency value?
To calculate PIC a MolKin v.3.0 software (Gutiérrez, et al. 2009) is quite friendly to use.
Another parameters can be calculated with: GenAlEx 6.5 software (Peakall, Smouse 2012), FSTAT v. 2.9.3.2 software (Gudet 2002) or GenePop v.4.0.10 software (Rousset, 2008). Good luck !
Your welcome dear Rupak
gene diversity is like PIC but yu can use this ref. : it is very useful
http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=0CDIQFjAB&url=http%3A%2F%2Firc.igd.cornell.edu%2FMolecularMarkers%2F04_Measures.pdf&ei=deEOU
Hello, all advices given are very good!.
From my experience, I recommend the use of PowerMarker software (http://statgen.ncsu.edu/powermarker/).
I hope you have luck. It is easy to use!.
Regards from Spain!,
Rocío.-
PIC = 1-∑ (Pi)2, where Pi is the proportion of samples carrying the ith allele of a particular locus is convenient to use for determining values for smaller populations or parental values only.....for larger populations use of software MolKin v.3.0 (Gutiérrez, et al. 2009) could be recommended.
I recommend the excel file you can calculate the PIC= 1-∑ (Pi)2. after write the equation you can estimate the allele frequency as x and try to estimate the X2 and then PIC= 1-∑ (Pi)2.
Polymorphic information content (PIC) is calculated for each marker using the following formula: PICi = 1-ΣP2ij, where Pij is the frequency of the jth allele in clone (i). You can use the excel file where you have to calculate first the ∑ (Pi)2, and after this you can calculate the PIC= 1-∑ (Pi)2. In my experience I tried useful GenAlEx 6.5 software (Peakall, Smouse 2012).
Yes, PowerMarker software (http://statgen.ncsu.edu/powermarker/) is recommended for PIC calculations.
The best option would be to calculate the PIC in an excel file using the following formula: PICi = 1-ΣP2ij. However, you can also use two programs under excel: Microsatellite Toolkit (http://genome-lab.ucdavis.edu/Links/Pop_Genet_ECL290/Week-1/download%20micro-toolkit.htm) or GenAlEx (http://biology.anu.edu.au/GenAlEx/Welcome.html). Or the PowerMarker software which is easy to use.
For PIC calculation of co-dominant markers like SSR, Cervus 3.0 is very good. It is user friendly. It gives heterozygosity and pic value for individual locus as well as an overall average value. Or you can use online PIC calculator- PicCalc
I also support the use of PowerMarker to compute PIC very easily. Reference: "Liu K, Muse SV (2005) PowerMarker: integrated analysis environment for genetic marker data. Bioinformatics 21: 2128-2129"
The software PowerMarker is easily. I am sending a guide (Attached).
by formula PICi = 1-ΣP2ij, where Pij is the frequency of the jth allele in clone (i). You can use the excel file where you have to calculate first the ∑ (Pi)2, and after this you can calculate the PIC= 1-∑ (Pi)2. In my experience I tried useful GenAlEx 6.5 software (Peakall, Smouse 2012).
PIC can be claculated by using the fallowing formulae
PICi=1-∑(Pij)2
Pij is the freuency of jth allele for i marker and the summation extends upto the total number of allele for the given marker.
Can someone please help me how i use Genealex to compute PIC because i dnt seem to see the function in my computer.
According to the following article
The PIC for SSR can be calculated using the formula below:
PICi=1-∑(Pi)2
Varshney, R.K., Chabane, K., Hendre, P.S., Aggarwal, R.K. and Graner, A., 2007. Comparative assessment of EST-SSR, EST-SNP and AFLP markers for evaluation of genetic diversity and conservation of genetic resources using wild, cultivated and elite barleys. Plant Science, 173(6), pp.638-649.
I also support the use of PowerMarker software to compute PIC values. Thanks.
Hi Dear Manoj Kumar Sharma
Thank you so much.
If you get PowerMarker software, Please kindly send for me.
Thanks
You can follow my page:-
https://www.researchgate.net/profile/M_El-Sayed2
Hi! Can someone kindly tell me where to find the PIC function in GenAlex?
Thank you
Well, I had a similar query a few months ago and finally calculated my PIC with MolKin software version 3.0 (Gutiérrez et al. 2005).
Thank you Justyna Anna Nowakowska ! Very easy to use! It was super helpful
Theoretically, PIC values can range from 0 to 1. At a PIC of 0, the marker has only one allele.
At a PIC of 1, the marker would have an infinite number of alleles. A PIC value of greater than 0.7 is considered highly informative, whereas a value of 0.44 is considered moderately informative. A gene or marker with only two alleles has a maximum PIC of 0.375.
Clearly, markers with greater numbers of alleles tend to have higher PIC values and thus are more informative.
@Reza Mohammadi,
Thank you for your clear explanation!
With regards!
- Badges
- Science method