RESEARCH ARTICLE


Primer1: Primer Design Web Service for Tetra-Primer ARMS-PCR



Andrew Collins1, *, Xiayi Ke2
1 Genetic Epidemiology and Genomic Informatics, School of Medicine, University of Southampton, Duthie Building (808), Southampton General Hospital, Southampton SO16 6YD, UK
2 MRC Centre of Epidemiology for Child Health and Centre for Paediatric Epidemiology and Biostatistics, 30 Guilford Street, London WC1N 1EH, UK


© 2012 Collins and Ke

open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: https://creativecommons.org/licenses/by/4.0/legalcode. This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

* Address correspondence to this author at the Genetic Epidemiology and Genomic Informatics, School of Medicine, University of Southampton, Duthie Building (808), Southampton General Hospital, Southampton SO16 6YD; Tel. 44 (0) 2380796939; Fax 44 (0) 2380794264; E-mail. arc@soton.ac.uk


Abstract

Tetra-primer ARMS-PCR is used extensively as a low cost, single PCR assay requiring no post-PCR manipulation. The design of successful primers depends on a number of variables such as melting temperatures, GC content, complementarity and selection of mismatch bases. The optimal selection of primers can be achieved in an automated way using a program which evaluates candidate primers for a given sequence. The Primer1 software was developed originally for use in the context of restriction fragment length polymorphism analysis using gel electrophoresis. However, recent applications have been more diverse, reviewed here, and we present an overview of the Primer1 software for primer design and web-service. We have updated the Primer1 program, and provide more complete details of the implementation. We also provide test data and output. The program is now available on a new, efficient, LAMP web service for users at: http://primer1.soton.ac.uk/primer1.html

Keywords: Javascript, mismatch base, primer design, single nucleotide polymorphism, tetra-primer ARMS-PCR, web service.