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Table 1 Free programs for PCR primer design.

From: Recent developments in primer design for DNA polymorphism and mRNA profiling in higher plants

Name Web source Ref. Note*
  General primer design   
Primer3 http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi [63] W
GeneFisher http://bibiserv.techfak.uni-bielefeld.de/genefisher/ [64] W
Primo Pro 3.4 http://www.changbioscience.com/primo/primo.html [65] W
PRIMO http://bioweb.pasteur.fr/seqanal/interfaces/primo.html [66] W
FastPCR http://www.biocenter.helsinki.fi/bi/Programs/fastpcr.htm [67] S
  Primer design based upon multi-alignments   
Primaclade http://dousta.umsl.edu/cgi-bin/primaclade.cgi [68] W
CODEHOP http://blocks.fhcrc.org/blocks/codehop.html [69] W
PriFi http://cgi-www.daimi.au.dk/cgi-chili/PriFi/main [70] W
  Primer design for single-nucleotide polymorphism (SNPs)   
IRA-PCR http://cedar.genetics.soton.ac.uk/public_html/primer2.html [71] W
SNP_Primers http://www2.eur.nl/fgg/kgen/primer/SNP_Primers.html [72] W
Primo SNP 3.4 http://www.changbioscience.com/primo/primosnp.html [65] W
  Primer design for Simple Sequence Repeat (SSR)   
SSR Finder http://bioinfo.agri.gov.il/cgi-bin/GE_SSR_Finder.pl [73] W
  Primer design for Microarrays   
ProbeWiz http://www.cbs.dtu.dk/services/DNAarray/probewiz.php [74] W
ROSO http://pbil.univ-lyon1.fr/roso/Home.php [75] W
OligoWiz 2 http://www.cbs.dtu.dk/services/OligoWiz2/ [76] S
Picky http://www.complex.iastate.edu/download/Picky/ [77] S
  Oligonucleotide properties calculation   
Oligo Analyzer http://www.idtdna.com/analyzer/Applications/OligoAnalyzer/ [78] W
Poland server http://www.biophys.uni-duesseldorf.de/local/POLAND/poland.html [79] W
NetPrimer http://www.premierbiosoft.com/netprimer/ [80] W
dnaMATE http://dna.bio.puc.cl/cardex/servers/dnaMATE/index.html [81] S/W
  1. *Note: W = Web-based; S = Standalone.