Tool name

Description

www

CODEHOP

Consensus Degenerate Hybrid Oligonucleotide Primers; degenerate PCR primer design; will accept unaligned sequences.

http://blocks.fhcrc.org/codehop.html

Gene Fisher

Interactive primer design tool for standard or degenerate primers; will accept unaligned sequences.

http://bibiserv.techfak.uni-bielefeld.de/genefisher/

DoPrimer

Easily design primers for PCR and DNA sequencing.

http://doprimer.interactiva.de/

Primer3

Comprehensive PCR primer and hybridization probe design tool; many options but easy to accept defaults at first.

http://www-genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi

http://www.basic.nwu.edu/biotools/Primer3.html

http://www.justbio.com/primer/index.php

Primer Selection

Select PCR primers from nucleotide sequence.

http://alces.med.umn.edu/rawprimer.html

Web Primer

Allow alternative design of primers for either PCR or sequencing purpose.

http://genome-www2.stanford.edu/cgi-bin/SGD/web-primer

PCR Designer

For restriction analysis of sequence mutations.

http://cedar.genetics.soton.ac.uk/public_html/primer.html

Primo Pro 3.4

Reduces PCR noise by lowering the probability of random primering.

http://www.changbioscience.com/primo/primo.html

Primo Degenerate 3.4

Primo Degenerate 3.4 designs PCR primers based on a single peptide sequence or multiple alignments of proteins or nucleotides.

http://www.changbioscience.com/primo/primod.html

PCR Primer Design

An application that designs primers for PCR or sequencing purposes.

http://pga.mgh.harvard.edu/servlet/org.mgh.proteome.Primer

The Primer Generator

The program analyzes the original nucleotide sequence and desired amino acid sequence and designs a primer that either has a new restriction enzyme site or is missing an old one.

http://www.med.jhu.edu/medcenter/primer/primer.cgi

EPRIMER3

Picks PCR primers and hybridization oligos (EMBOSS).

http://bioweb.pasteur.fr/seqanal/interfaces/eprimer3.html

PRIMO

Prediction of forward and reverse oligonucleotide Primers.

http://bioweb.pasteur.fr/seqanal/interfaces/primo.html3

http://atlas.swmed.edu/primo/primo_form.html

PrimerQuest

A primer design tool.

http://www.idtdna.com/biotools/primer_quest/primer_quest.asp

MethPrimer

Design primers for methylation PCRs.

http://itsa.ucsf.edu/~urolab/methprimer/index1.html

Rawprimer

A tool for selection of PCR primers.

http://alces.med.umn.edu/rawprimer.html

MEDUSA

A tool for automatic selection and visual assessment of PCR primer pairs.

http://www.cgr.ki.se/cgr/MEDUSA/

The Primer Prim'er Project

Software suite that completely
automates the PCR primer design process.

http://www-nmr.cabm.rutgers.edu/bioinformatics/Primer_Primer_

Project/Primer.html

Oligonucleotides for the PCR

Seek oligonucleotides on both sides of an area.

http://www.citi2.fr/bio2/Oligo2lib.html

GAP

Genome- wide Automated Primer finder servers.

http://promoter.ics.uci.edu/Primers/