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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.
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Plant Methods

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