Methods to detect SNPs

There are several methods to SNP identification.
SNP identification can be categorized in to 2 main sub sets.
1. Novel SNP detection.
2. Simply detecting the known SNPs.

For novel snp detection sequencing will be the best method. In this we will select the region which we want to screen for snps from a public database like Ensembl and/or NCBI and we will sequence the region using primers which are specific for that particular region. Once we sequence the region of interest (ROI) we have to compare the sequence to the preexisting sequence to see the variations(SNPs). Here we will get a doubt if we don't have a previous sequence knowledge of that ROI the how can we identify the SNPs. In such case if you are the first person to perform the sequence analysis for that ROI then you have to do the same thing with some other samples after that compare all the sequence to each other and then you will come to know whether there is any variation present in that ROI. To do this we have to use sequence alignment softwares. These softwares align sequences to each others, by doing this we can compare them very fast and very easily. Once we get an idea about the SNp sites in our ROI the we can go for known SNP detection.
Known SNP detection is also known as SNP genotyping. There are several methods available for this. We will discuss about them in future.

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