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ABSTRACT:
Summary: One of the most essential roles in polymerase chain reaction (PCR) primer design is a gene structure, predominantly for eukaryotic cells genes with numeral single-nucleotide polymorphisms (SNPs) which impose on users the discrimination between them via many techniques involving PCR. At this point, PRIMER1 is illustrated as suitable network server used for primer design to detect SNP by a simple and economical method named tetra-primer amplification refractory mutation system-polymerase chain (ARMS-PCR). In PRIMER1, the users are able to concentrate their attention on the dbSNP nCbI and primer design delineation without wasting time identifying the positions of SNPs manually configuring difficult limitation. Accessibility: PRIMER1 is freely accessible at: http://primer1.soton.ac.uk/primer1.html. The network server supports the browsers: Firefox, Chrome, Safari, Opera, and Torch.
KEYWORDS: SNP, Tetra-ARM-PCR, SBE, dbSNP.
A. INTRODUCTION
In eukaryotic genes, different SNPs are commonly found, and they play essential roles in genetic variation among people, and can act as biological indicators, helping scientists to set genes that are linked with disease (1). SNP in both sides for the primer design to discriminate it specifically. Accessible programs, like Primer3 (2), and SNP masker (3), are needed frequently by users to upload, paste and manually specify the DNA sequence involving SNP. Significantly, none of these programs supports detecting specific SNP without using restriction enzyme. On the other hand, the visualization of exact SNP position makes a more direct impression and gives users further information on the spatial associations than the currently used.
In fact, new technological tools are developed rapidly, mainly HTML5 and JavaScript, making users familiar with designing more accurate and accepted primer for PCR.
The complicated primer designing options can be excluded or modified by a number of mouse clicks process.
Therefore, the researcher recommends PCR Designer for Restriction Analysis of SNPs, a web server for imagination PCR primer design on well-known reference SNP ID number ("rs#"; "refSNP cluster"). There are many prosperities that distinguish PCR Designer for Restriction Analysis of SNP genotype from other conventional PCR primer design programs: a) pasting the template DNA sequence, T-ARMS-PCR recognize FASTA sequence from dbSNP NCBI; b) Normal first allele as indicated in...