PCR designer for restriction analysis of various types of sequence mutation

Abstract

Restriction analysis is widely used to detect gene mutations such as insertions, deletions and single nucleotide polymorphisms (SNPs). Although such mutation sites sometimes present some natural restriction sites to differentiate the wild-type and mutant sequences, mismatches are often needed in order to create artificial restriction fragment length polymorphisms (RFLPs). In this report, a computer program is described that screens for suitable restriction enzymes, introducing mismatches where appropriate and when necessary, designs primers using the information of the selected restriction enzymes, their recognition sequence and locations as well as the information about the mismatches if any. The program, supported by a WWW web interface, is intended to be used online.