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.

MRPrimerW2 – Search valid Primers for multiple Targets of qPCR experiments without matching Off-targets

MRPrimerW2

:: DESCRIPTION

The MRPrimerW server performs complete homology testing, supports batch design of primers for multi-target qPCR experiments, and ranks the resulting primers to return the top-1 best primers to the user.

::DEVELOPER

Infolab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 MRPrimerW

:: MORE INFORMATION

Citation

Jeon H, Bae J, Hwang SH, Whang KY, Lee HS, Kim H, Kim MS.
MRPrimerW2: an enhanced tool for rapid design of valid high-quality primers with multiple search modes for qPCR experiments.
Nucleic Acids Res. 2019 Jul 2;47(W1):W614-W622. doi: 10.1093/nar/gkz323. PMID: 31045205; PMCID: PMC6602510.

MRPrimerW: a tool for rapid design of valid high-quality primers for multiple target qPCR experiments.
Kim H, Kang N, An K, Koo J, Kim MS.
Nucleic Acids Res. 2016 May 6. pii: gkw380.

AMUSER 1.0 – Design of Optimal PCR Primers for USER Cloning

AMUSER 1.0

:: DESCRIPTION

AMUSER (Automated DNA Modifications with USER cloning) offers quick and easy design of PCR primers optimized for various USER cloning based DNA engineering

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Software-Supported USER Cloning Strategies for Site-Directed Mutagenesis and DNA Assembly.
Genee HJ, Bonde MT, Bagger FO, Jespersen JB, Sommer MO, Wernersson R, Olsen LR.
ACS Synth Biol. 2015 Mar 20;4(3):342-9. doi: 10.1021/sb500194z.

HYDEN – A software for Designing Degenerate Primers

HYDEN

:: DESCRIPTION

HYDEN (HighlY DEgeNerate primers) is a program for designing pairs of degenerate primers for a given set of DNA sequences. HYDEN works well for large input sets of genomic sequences (e.g., hundreds of sequences of length 1Kbp).

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 HYDEN

:: MORE INFORMATION

Citation

Degenerate primer design: theoretical analysis and the HYDEN program.
Linhart C, Shamir R.
Methods Mol Biol. 2007;402:221-44.

GSP – Genome Specific Primers Design in Polyploid Species

GSP

:: DESCRIPTION

GSP is a web-based platform to design genome-specific primers that distinguish subgenome sequences in a polyploid genome.

::DEVELOPER

GSP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GSP

:: MORE INFORMATION

Citation

GSP: a web-based platform for designing genome-specific primers in polyploids.
Wang Y, Tiwari VK, Rawat N, Gill BS, Huo N, You FM, Coleman-Derr D, Gu YQ.
Bioinformatics. 2016 Mar 9. pii: btw134.

PrecisePrimer – Designing PCR Primers for DNA library Cloning and DNA Shuffling

PrecisePrimer

:: DESCRIPTION

PrecisePrimer is a web-based primer design software made to assist experimentalists in any repetitive primer design task such as preparing, cloning and shuffling DNA libraries.

::DEVELOPER

Jean-Loup Faulon’s group at Micalis.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W205-9. doi: 10.1093/nar/gku393. Epub 2014 May 14.
PrecisePrimer: an easy-to-use web server for designing PCR primers for DNA library cloning and DNA shuffling.
Pauthenier C, Faulon JL

FastPCR 6.5.55 – PCR Primers or Probe Design

FastPCR 6.5.55

:: 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.

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

Beacon Designer 8.14 – Automate Real Time PCR Primer & Probe Design

Beacon Designer 8.14

:: 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