Primer3 2.4.0 / Primer3-web 4.1.0 / Primer3Plus 2.5.0 – PCR Primer Design Tool

Primer3 2.4.0 / Primer3-web 4.1.0 / Primer3Plus 2.5.0

:: DESCRIPTION

Primer3 is a widely used program for designing PCR primers (PCR = “Polymerase Chain Reaction”). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers.

Primer3-web is the original web-interface to Primer3.

Primer3Plus is an updated, task-oriented web-interface to Primer3.

::DEVELOPER

developed at Whitehead_Institute and Howard Hughes Medical Institute by Steve Rozen and Helen Skaletsky.

:: SCREENSHOTS

:: REQUIREMENTS

- Linux / Windows / Mac OsX

perl

:: DOWNLOAD

Primer3

:: MORE INFORMATION

Citation

Steve Rozen and Helen J. Skaletsky (2000)
Primer3 on the WWW for general users and for biologist programmers.
In: Krawetz S, Misener S (eds) Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana Press, Totowa, NJ, pp 365-386

LAMP Designer 1.16 – Design Primers for Loop-Mediated Isothermal Amplification Assays

LAMP Designer 1.16

:: DESCRIPTION

LAMP Designer designs efficient primers for Loop-Mediated Isothermal Amplification assays, that amplify DNA and RNA sequences at isothermal conditions, eliminating the necessity of a PCR setup. The technology relies on auto-cycling and DNA polymerase mediated strand displacement DNA synthesis, amplifying a few copies of DNA to 109 in less than an hour. Reverse transcription coupled LAMP can be applied for amplification of RNA sequences.

::DEVELOPER

PREMIER Biosoft

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

LAMP Designer Demo

:: MORE INFORMATION

AmplifX 2.1.1 – Manage & Design Primers for PCR

AmplifX 2.1.1

:: DESCRIPTION

AmplifX is a software to search through a collection of primers, such as any molecular biologist has in his refrigerators, to find those which can be use to amplify a fragment into a target sequence, for example, and particularly, to design strategies to screen recombinant clones by PCR. Some information is associated with each primer; some automaticelly computed by AmplifX (like TM, Quality, length) and others given by the user (name, comments,…) This allows general aspects of primer management (sequences and real tubes). AmplifX can also design new primers.

::DEVELOPER

Nicolas Jullien

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOSX / Linux

:: DOWNLOAD

AmplifX

:: MORE INFORMATION

PRISE – Designing Sequence-selective PCR Primers

PRISE

:: DESCRIPTION

PRISE (PRImer Selector) is an interactive software package for PCR primer design. PRISE enables the design of sequence-specific / sequence-selective PCR primers. One important feature of PRISE is that it automates the task of placing primer-template mismatches at the 3′ end of the primers – a property that is crucial for sequence selectivity / specificity

::DEVELOPER

Rachid Ounit, Algorithms and Computational Biology Lab ,University of California

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

PRISE

:: MORE INFORMATION

Citation

J Microbiol Methods. 2008 Mar;72(3):263-7. doi: 10.1016/j.mimet.2007.12.004.
PRISE (PRImer SElector): software for designing sequence-selective PCR primers.
Fu Q1, Ruegger P, Bent E, Chrobak M, Borneman J.

PrimerSeq 1.1.12 – Primer Seek in RNA-Seq

PrimerSeq 1.1.12

:: DESCRIPTION

PrimerSeq designs RT-PCR primers that evaluate alternative splicing events by incorporating RNA-Seq data.

::DEVELOPER

Xing Lab

:: SCREENSHOTS

:: REQUIREMENTS

Windows/MacOsX

:: DOWNLOAD

PrimerSeq

:: MORE INFORMATION

Citation

PrimerSeq: Design and visualization of RT-PCR primers for alternative splicing using RNA-seq data.
Tokheim C, Park JW, Xing Y.
Genomics Proteomics Bioinformatics. 2014 Apr;12(2):105-9. doi: 10.1016/j.gpb.2014.04.001.

Beacon Designer 8.21 – Automate Real Time PCR Primer & Probe Design

Beacon Designer 8.21

:: DESCRIPTION

Beacon Designer™ automates the design of real time primers and probes. It is used by molecular biologists worldwide to design successful real time PCR assays. It saves the time and the money involved in failed experiments. Beacon Designer™ is a flexible solution to your real time primer and probe design needs and pays for itself many times over.

::DEVELOPER

PREMIER Biosoft

:: SCREENSHOTS

:: REQUIREMENTS

MacOsX / Windows

:: DOWNLOAD

Beacon Designer Demo

:: MORE INFORMATION

Oligo 7.60 – Primer Analysis Software

Oligo 7.60

:: DESCRIPTION

OLIGO Primer Analysis Software is the essential tool for designing and analyzing sequencing and PCR primers, synthetic genes, and various kinds of probes including siRNA and molecular beacons. Based on the most up-to date nearest neighbor thermodynamic data, Oligo’s search algorithms find optimal primers for PCR, including TaqMan, highly multiplexed, consensus or degenerate primers. Multiple file batch processing is possible. It is also an invaluable tool for site directed mutagenesis. OLIGO performs a range of functions for researchers in PCR and related technologies; consensus, multiplex and degenerate primers, oligonucleotide database, secondary structure, LCR and more.

::DEVELOPER

Molecular Biology Insights

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOSX

:: DOWNLOAD

Oligo

:: MORE INFORMATION

PrimerFactoryQt 1.0.3 beta- Tool for Searching and Designing Primers

PrimerFactoryQt 1.0.3 beta

:: DESCRIPTION

PrimerFactoryQt is a tool for searching and designing primers. The Primer Search is based on Bowtie, an ultrafast, memory-efficient alignment program for aligning short DNA sequence. You can build your specific oligo database and search it against your query sequence. Consequently you find out, where your available primers will bind. Laboriously quests or new ordering of oligos is not anymore required. In addition you can save the search hits as features in a genbank file format.

::DEVELOPER

Stefanie Lück

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

PrimerFactoryQt

:: MORE INFORMATION

FastPCR 6.7.50 – PCR Primers or Probe Design

FastPCR 6.7.50

:: DESCRIPTION

FastPCR software has integrated tools environment that provide comprehensive facilities for designing primers for most PCR applications including standard, long distance, inverse, real-time, multiplex, unique and group-specific; overlap extension PCR (OE-PCR) multi-fragments assembling cloning; single primer PCR (design of PCR primers from close located inverted repeat), automatically SSR loci detection and direct PCR primers design, amino acid sequence degenerate PCR, Polymerase Chain Assembly (PCA) or oligos assembly and much more.The “in silico” (virtual) PCR primers or probe searching, comprehensive pairs and individual primers analysis tests are included. The “in silico” oligonucleotide search is helpful for discovering target binding sites with the temperature melting calculation.

::DEVELOPER

PrimerDigital

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

FastPCR

:: MORE INFORMATION

Citation

Methods Mol Biol. 2014;1116:271-302. doi: 10.1007/978-1-62703-764-8_18.
FastPCR software for PCR, in silico PCR, and oligonucleotide assembly and analysis.
Kalendar R1, Lee D, Schulman AH.

Kalendar R, Lee D, Schulman AH 2009.
FastPCR Software for PCR Primer and Probe Design and Repeat Search.
Genes, Genomes and Genomics, 3(1): 1-14.

MFEprimer 3.2.1 – PCR Primer Specificity Checking Program

MFEprimer 3.2.1

:: DESCRIPTION

MFEprimer : Multiple factor evaluation of the specificity of PCR primers. This program is designed to evaluate the specificity of PCR primers based on known multiple factors including sequence similarity, stability at the 3’end of the primer, melting temperature, GC content, and number of binding sites between the primers and DNA templates. It can help the user to select more suitable primers before running either standard or multiplex PCR reactions.

::DEVELOPER

Wubin Qu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

MFEprimer

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W205-8. doi: 10.1093/nar/gks552. Epub 2012 Jun 11.
MFEprimer-2.0: a fast thermodynamics-based program for checking PCR primer specificity.
Qu W1, Zhou Y, Zhang Y, Lu Y, Wang X, Zhao D, Yang Y, Zhang C.

Wubin Qu, Zhiyong Shen, Dongsheng Zhao, Yi Yang and Chenggang Zhang. (2009)
MFEprimer: multiple factor evaluation of the specificity of PCR primers,
Bioinformatics, 25(2), 276-278.