BIOINFORMATICS APPLICATIONS NOTE Genome analysis ExPrimer: to design primers from exon–exon junctions

Abstract

Summary: ExPrimer is a web-based computer program to design primers mainly from a specified exon–exon junction (E-E-jn) of a gene of interest. The tool suggests the optimum primer-pair(s) of which the right (reverse) primer represents a particular E-E-jn of the mRNA. The ‘product length ’ decides the location of the left primer. The results also include all other primer pairs considered and their ‘scores’. ExPrimer can use the NCBI BLASTn program for sequence specificity of primers. The tool is useful in many areas of molecular biology research that involve hybridization of short sequences with mRNA or cDNA. Availability