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Primer Design Tools and Oligo Software :

Software, programs, and online bioinformatic tools for the design of primers and oligonucleotides.

We recommend the following:

Array Designer Premier Biosoft International. Software which can design primers for DNA or oligo arrays.

Beacon Designer Premier Biosoft International.

OligoArray2.1 OligoArray 2.0 and the new version 2.1 are free software packages that compute gene specific oligonucleotides for
     genome-scale oligonucleotide microarray construction. Reference [PubMed] Free

Oligodb - Oligodb is a web-based program for the interactive design of DNA oligos for transcription profiling and hybridization of human genes. The oligodb program determine oligos using human DNA-transcript data from ENSEMBL. Reference [PubMed][pdf]

OligoPicker - OligoPicker can select up to five oligo probes for each of the DNA sequences you provide for microarray spotting. Reference [PubMed] Free

PrimerQuest Free

Genome-wide Automated Primer finder servers (GAP) Software which can design thousands of primer pairs to amplify a set of open reading frames (ORFs) covering a whole genome. Free

Genome PRIDE GenomePRIDE is a primer design software tool that designs PCR primers or long oligos based on annotated sequences.
GenomePRIDE has been used for the design of many DNA arrays/chips. Free

Primer3 Whitehead Institute/MIT Center for Genome Research, Free

Primer Premier Premier Biosoft International.

PRIMEGENS- Primegens (Primer Design Using Gene Specific Fragments) is a computer program which you use selected gene-specific fragments and then it designs primer pairs for PCR amplifications. Reference [PubMed]

ProbeWiz Server - The CBS ProbeWiz WWW server predicts optimal PCR primer pairs for generation of probes for cDNA arrays. Reference [PubMed]

ProMide - ProMide is a collection of command-line tools for Probe selection and Microarray Design. Free

Sarani - Sarani Gold (Genome Oligo Designer) is a software for automatic large-scale design of optimal oligonucleotide probes for microarray experiments. Thousands of gene sequences can be analyzed together and best available oligonucleotide probes with uniform thermodynamic properties and minimal similarity to non-specific genes can be selected. Product of Strand Genomics.

STACKdb - The STACKdb, Sequence Tag Alignment and Consensus Knowledgebase, is generated by processing EST and mRNA sequences obtained from Genbank through a pipeline consisting of masking, clustering, alignment and variation analysis steps. The STACKdb database is created using tools called "stackPACK". Also available through Electric Genetics. Free

Visual OMP - Visual OMP picks primers and oligo probes which do not cross hybridize with each other and other targets. Uses the OMP (Oligonucleotide Modeling Platform) engine, based on scientific research by nucleic acids thermodynamics expert, Dr. John SantaLucia.  DNA Software, Inc.

WebPrimer Free

Xpression Primer Premier Biosoft International.