Primer Design Tools
AMOD	a tool for designing antisense morpholino oligonucleotides
Array Designer	can design hundreds of primer for DNA or oligonucleotide microarrays
ASePCR	a tool for carrying out e-PCR to detect differences in amplicon sizes in transcripts
PCR Oligo Maker	a tool for designing PCR probes based construction of long DNA molecules
autoprime	amplifies  cDNA generated from mRNA but not genomic DNA
calculator	Oligonucleotide Calculator
cDNA primers	for creating primers around the Open Reading Frame of cDNAs
codehop	primers designed from protein multiple sequence align
CODEHOP	generates  Hybrid Oligonucleotide Primers; degenerate PCR primer design
DEQOR	aids in the design and quality control of small interfering RNAs (siRNAs)
DINAMelt	a tool for predicting hybridization and folding of DNA and RNA
DoPrimer	web based primer design
Electronic PCR	Find STS map location in a DNA sequence of interest; useful for detecting mis-priming events
ELXR	exon locator and extractor
E-RNAi	a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments
exon primer perl script	design primers based on Perl script
ExonPrimer	helps to design intronic primers for the PCR amplification of exons
FastPCR	design of PCR primers for standard and long PCRs, inverse PCR
Gene2Oligo	divides both strands of DNA sequence into a set of contiguous oligonucleotides
Genefisher	nteractive primer design tool for standard or degenerate primers
GeneWalker	allows you to work with two primer sequences simultaneously
genomic primer	for creating primers around exons in genomic DNA
GenoPlante	For high-throughput design
MethPrimer	Design Primers for Methylation PCRs
MuPlex	a tool to assist in the design of multiplex PCR assays
Oligo Calculator	oligo calculator
OligoArray2	computes gene specific oligonucleotides for genome-scale oligonucleotide microarray
OligoChecker	Verifies the Specificity of Batch Oligo Designs
Oligodb	generates oligos suitable for expression experiments
OligoPicker	picks specific oligos by skipping regions with contiguous bases common in other sequences.
OligoWiz	allows for the integration of sequence annotations
OligoWiz 2 Server	intelligent design of oligonucleotides for DNA microarrays
PCR Guide	guide
PCR now	A Real-Time PCR Primer Design Tool
pcr suite	collection of programs that interact with primer 3.0
PDA	primer design
PerlPrimer	open-source PCR primer design
Pride	automatically designs primers
PriFi	a tool for designing and evaluating primer pairs
Primaclade	accepts a multiple species nucleotide alignment file as input
PRIMEGENS	selecst gene-specific fragments and then design primer pairs using Primer3 for PCR amplifications
primer design	list of primer software
Primer Generator	an automated generator of primers for site-directed mutagenesis
primerbank	a public resource for PCR primers
PrimerPremier	design primer pairs for PCR and multiplex experiments
PrimerX	Automated design of mutagenic primers for site-directed mutagenesis
primo	from ChangBioscience
ProbeLynx	allows users to assess the specificity of probe sequences used for microarray experiments
PROBEmer	Primer Design for Target Families
ProbeWiz Server	predicts optimal PCR primer pairs for generation of  probes for cDNA arrays
ProMide	ProMide is a collection of command-line tools for Probe selection
PUNS	assists in the specificity design of PCR primers
QPPD	contains information about primer sets published for quantitative PCR
Sfold	aiding the design of short interfering RNAs
siDirect	for computing siRNA sequences
siRNA Selection Server	design of short interfering RNAs (siRNAs)
SNPbox	does large-scale standardized primer design
TGGE-star	designs primers fulfilling the requirements for a sensitive mutation screening
TROD	for short interfering RNA (siRNA) synthesis with T7 RNA polymerase
Vector NTI	PCR primer design
Visual OMP	multiplex primer and probe design optimized to reduce cross-hybridization.
webprimer	primer design