OLIGO Primer Analysis Software was the first publicly-available software for DNA

DNA

Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...

 primer design. The first papers describing this software were published in 1989 and 1990, and consecutive upgrades in the 1990-s and 2000-s, all have been cited together over 600 times in scientific journals and over 500 times in patents (according to Scopus

Scopus

Scopus, officially named SciVerse Scopus, is a bibliographic database containing abstracts and citations for academic journal articles. It covers nearly 18,000 titles from over 5,000 international publishers, including coverage of 16,500 peer-reviewed journals in the scientific, technical, medical,...

). The program is a comprehensive real time PCR primer and probe search and analysis tool, and also does other tasks such as siRNA

Sírna

Sírna Sáeglach , son of Dian mac Demal, son of Demal mac Rothechtaid, son of Rothechtaid mac Main, was, according to medieval Irish legend and historical tradition, a High King of Ireland...

 and molecular beacon

Molecular beacon

Molecular beacons are oligonucleotide hybridization probes that can report the presence of specific nucleic acids in homogenous solutions. The terms more often used is molecular beacon probes. Molecular beacons are hairpin shaped molecules with an internally quenched fluorophore whose fluorescence...

 searches, open reading frame

Open reading frame

In molecular genetics, an open reading frame is a DNA sequence that does not contain a stop codon in a given reading frame.Normally, inserts which interrupt the reading frame of a subsequent region after the start codon cause frameshift mutation of the sequence and dislocate the sequences for stop...

 and restriction enzyme

Restriction enzyme

A Restriction Enzyme is an enzyme that cuts double-stranded DNA at specific recognition nucleotide sequences known as restriction sites. Such enzymes, found in bacteria and archaea, are thought to have evolved to provide a defense mechanism against invading viruses...

 analysis etc. It has been created and maintained by Wojciech Rychlik

Wojciech Rychlik

Wojciech Rychlik is a biologist and photographer, born in Poland and living in the USA since 1980. Rychlik received his Ph.D. in 1980 from the Polish Academy of Sciences. Currently, he is a president of Molecular Biology Insights, Inc. located in Cascade, Colorado.The main focus of Rychlik's...

 and Piotr Rychlik. The OLIGO has been reviewed several times in scientific journals, for the first time in 1991 in a review in Critical Reviews in Biochemistry and Molecular Biology, and for its next upgrades (with OLIGO 7 being the latest one in 2011).

Oligo Primer Analysis Software has been used in various scientific studies (as cited by examples of recent publications), among them for: real time PCR, apoptosis studies, antigen typing, species identification, studies on species evolution, measuring mRNA expression levels, oligonucleotide-based array hybridization studies, degenerate primer studies, microsatellite analysis, DNA microarray detection, inverse PCR, genome walking, nucleotide polymorphisms studies, detection of microorganisms or viruses, genotyping, cloning, vector (gene) construction, genome sequencing, detection of mutants or intraspecific variability, genetic disease studies, siRNA and gene silencing, FISH analysis (single cell expression study), scorpion probes, and development of new DNA amplification methods.

Other Primer Design Software

• AutoDimer
• FastPCR
• GeneFisher2
• Gene Designer
  Gene Designer
  Gene Designer is a free bioinformatics software package. It is used by Molecular Biologists from academia, government and the pharmaceutical, chemical, agricultural and biotechnology industries to design, clone and validate genetic sequences.- Features :...
  
  
• Geneious
  Geneious
  Geneious is suite of cross-platform bioinformatics software applications developed by Biomatters Ltd.- Features :Geneious comes in a Basic version that is free for academic use, and a commercial Pro version with added features. Geneious bundles various bioinformatics tools under one hood with an...
  
  
• GenScript Real-time PCR
• iCODEHOP
• MacVector
  MacVector
  MacVector is a commercial sequence analysis application for Apple Macintosh computers running Mac OS X. It is intended to be used by Molecular Biologists to help analyze, design, research and document their experiments in the laboratory.- Features :...
  
  
• Netprimer
  Netprimer
  NetPrimer is a free web based tool used for analyzing primers used in PCR to amplify a DNA sequence. The software predicts the melting temperature of the primers using the nearest neighbor thermodynamic algorithm...
  
  
• Oligo Calc
• OligoAnalyzer
• Picky
• Primer Premier
  Primer Premier
  Primer Premier software combines design of primers for various PCR applications under one common platform. The software supports design of degenerate primers on alignments for amplifying related set of nucleotide sequences for detecting common traits among organisms and to determine heredity. The...
  
  
• Primer-BLAST
• Primer3
• Primer3Plus
• PrimerX
• The PCR Suite
• UGENE
  UGENE
  UGENE is free open-source cross-platform bioinformatics software.It integrates dozens of well-known biological tools and algorithms, providing both graphical user and command line interfaces...
  
  
• Vector NTI
  Vector NTI
  Vector NTI is a bioinformatics software package. The current versions are v11.5.1 for Windows/PCs and v7.1 for Macs, but only supporting Mac OS X v10.3 .- Features :* create, annotate, analyse, and share DNA/protein sequences...
  
  
• Visual OMP
• Web Primer

For more information about primer analysis freeware, please see the Primer entry.