Auto Primer3 Files

The programs available here invoke primer3 (http://primer3.sourceforge.net/) in order to design primers to amplify exons of human RefSeq genes. The user only needs to know the name of the gene or transcript they are interested in.

In the case of the Windows and Mac OS X GUI applications the hg19 build of the human genome is used as the genomic reference sequence. dbSNP135 reference files were used to allow a program specific mask of SNPs from primer designs (build 131 or with a MAF of 1 % or higher). 

For the stand alone script you are responsible for downloading the appropriate reference files from the UCSC genome browser - you will need the fasta format chromosome sequences (e.g. extracted from the appropriate chromFa.tar.gz from http://hgdownload.cse.ucsc.edu/downloads.html), the corresponding refGene.txt reference file and a dbSNP vcf file. More details are available in the scripts documentation which can be accessed using 'perldoc auto_primer3.pl' or 'perl auto_primer3.pl -m'. You will also need to install primer3 (http://primer3.sourceforge.net/) and download the appropriate mispriming library. 

Auto Primer3 does use a repeats mispriming library to avoid designing to repetitive regions. However, it does not check for pseudogenes or blat the primers to ensure they do not match multiple locations.

primer3 is open source software available at http://primer3.sourceforge.net/,  Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006,2007 Whitehead Institute for Biomedical Research, Steve Rozen, and Helen Skaletsky. All rights reserved.

The rest of the application was written by Dr David Parry at the University of Leeds and is distributed free of charge under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.