MSR Calcalate

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Firstly, what’s MSR? MSR is an abbreviation for Methylation Share Rate. MSR index is an epigenetic parameter and it will better reflect the DNA methylation modification level for different regions within genes in animals and plants. 
  Secondly, what’s the equation of MSR index? According to the data analysis model of random amplified polymorphic DNA (RAPD) marker (Welsh and McClelland, 1990; Williams et al., 1990), methylated-DNA-fingerprint similarity is generally defined as methylated share rates (MSR). The genetic similarity (S) or methylated share rates (MSR) was determined by Nei and Lynch’s method (Nei and Li, 1979; Lynch, 1990): MSR= 2NAB/(NA + NB), where “NAB” is the number of methylation that colony A and B shared in common, “NA” is the number of methylation in colony A and “NB” is the numbers of methylation in colony B. The mean MSRs and their standard deviation, standard error was carried out by C++ protocol which was designed by our group.
  Thirdly, why MSR was put up. MSR was firstly created to evaluate methylation level, which was enlightened by the fraction of brands share rate (BSR) of the RAPD model. (1) the C-methylation and C-unmethylation of the specific CpG-dinucleotide locus is random, which similarly complied with the character of the RAPD marker. These phenomena were listed as follows: (a) methylation or unmethylation status randomly occurred in different positive colonies from the same individual in all analyzed samples; (b) For the CpG-dinucleotide loci, sometimes 100% methylation loci randomly presented in different loci; (c) there were significant differences of CpG-dinucleotide methylation in different positive colonies from the same individual. (2) the C-methylation or C-unmethyatlin in cytosine is co-domination, which was identical with the RAPD marker, because the single positive insert only bring one haplotype. (3) the methylation of individuals being compared was run with adequate controls, to minimize the errors in assigning identity to methylation pairs. (4) all individuals were to be relatively random members of the population. (5) the marker loci are to be unlinked and in Hardy-Weinberg equilibrium within and between loci. 
  Fourthly, what advantages of MSR have. As we know, bisulfite sequencing (BSP) technology is a “gold standard” for detecting the DNA methylation level of different regions within genes. When the BSP method was used in DNA methylation in epigenetics, the methylation percentage (MP) has been widely used in DNA methylation analysis. However, when methylation percentage (MP) is used in BSP method, a lot of potential and important information for DNA methylation will miss because MP just reflects the percentage using the ratio of methylated Cytosine (C) vs unmethylated Cytosine (C) in spite of other comprehensive information, such as  CpG-dinucleotide loci, colonies, individuals and populations. While the MSR index will effectively evaluate the methylated information beyond the methylation percentage. Because MSR equation includes all types of above-mentioned comprehensive data sources, such as CpG-dinucleotide loci, colonies, individuals and populations. Therefore, MSR has more advantages when compared with MP, and is strongly recommended to be a useful and effective index to evaluate the DNA methylation level as well as the MP index.
  Fifthly, who develop this MSRcall software and website. The MSRcall software is a web-based platform for analyses of MSR (methylated share rate) index according to C++ protocol. This MSRcall home is developed by Lan_Liu’ group: Ph.D. Xianyong Lan (From College of Animal Science and Technology, Northwest A&F University) and Ph.D. Liangliang Liu (From Jiangsu university of Science and Technology).  
  If you want to know more information about MSR and MSRcall, please download our published paper: “Pan C, Jia W, Wu X, Zhao H, Liu S, Lei C, Lan X*, Chen H. DNA methylation profile of caprine Dnmt3b gene and its influence on growth traits. The Journal of Animal & Plant Sciences, 2013, 23 (2): 380-387”. If you use the MSR for research study, please cite above-mentioned literature. If you use the MSRcall online website to calculate the MSR index, please cite our website: www.msrcall.com. Thanks a lot. 
  Any question, please contact  Ph.D. Xianyong Lan (lan342@126.com) and Ph.D. Liangliang Liu(lingyun79626@126.com).

input data upload file

Caution: The format of input data should be(!!!)

Caution: The format of input data should be --

1,0,0,0,0,0,0,1, ,1,1...

1,0,0,0,0,1,1, ,1,1,0...

0,1,0,0,0,1,0,0,0,0,0...

...

here first,each row of data is composed of 1 or 0 or space;

second,each character separated by commas(half-angle state);

third,the last character should be 1 or 0 or space;

last,all lines should be the same number of characters,if there are missing characters an the end of a line,we will use space instead;

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