PrimerProspector 1.0.1 – Design and Analyze PCR Primers

PrimerProspector 1.0.1

:: DESCRIPTION

PrimerProspector is an open-source software package that allows researchers to develop new primers from collections of sequences and to evaluate existing primers in the context of taxonomic data.

::DEVELOPER

Knight Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python
  • PyCogent
  • Numpy
  • Matplotlib

:: DOWNLOAD

 PrimerProspector

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Apr 15;27(8):1159-61. doi: 10.1093/bioinformatics/btr087.
PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers.
Walters WA, Caporaso JG, Lauber CL, Berg-Lyons D, Fierer N, Knight R.

qRTDesigner 1.2 – Designing Primers for Real-time Quantitative PCR Assays

qRTDesigner 1.2

:: DESCRIPTION

qRTDesigner is a program for designing primers for real-time quantitative PCR assays.

:DEVELOPER

Department of Bioinformatics, University of Tartu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

PLoS One. 2015 Apr 8;10(4):e0122713. doi: 10.1371/journal.pone.0122713. eCollection 2015.
Haplotype phasing and inheritance of copy number variants in nuclear families.
Palta P, Kaplinski L, Nagirnaja L, Veidenberg A, Möls M, Nelis M, Esko T, Metspalu A, Laan M, Remm M

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

MRPrimerW

:: 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 DGIST.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 MRPrimerW

:: MORE INFORMATION

Citation

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.

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

HTP-OligoDesigner – An Online Primer Design Tool

HTP-OligoDesigner

:: DESCRIPTION

HTP-OligoDesigner was created to provide the scientific community with a simple and intuitive online primer design tool for both laboratory-scale and high-throughput projects of sequence-independent gene cloning and site-directed mutagenesis and a Tm calculator for quick queries.

:: DEVELOPER

HTP-OligoDesigner team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

J Comput Biol. 2016 Jan;23(1):27-9. doi: 10.1089/cmb.2015.0148. Epub 2015 Nov 5.
HTP-OligoDesigner: An Online Primer Design Tool for High-Throughput Gene Cloning and Site-Directed Mutagenesis.
Camilo CM, Lima GM, Maluf FV, Guido RV, Polikarpov I.

PCR Analyzer v 1.02 – Estimate for Initial Amount of Amplicon Present in a PCR

PCR Analyzer v 1.02

:: DESCRIPTION

PCR Analyzer is a software to estimate the initial amount of amplicon using a simplified mechanistic model based on chemical reactions in the annealing step of the PCR.

::DEVELOPER

National Institute of Environmental Health Sciences , National Institute of Health

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

PCR Analyzer

:: MORE INFORMATION

Citation

Marjo V Smith , Chris R Miller, Michael Kohn, Nigel J Walker and Chris J Portier
Absolute estimation of initial concentrations of amplicon in a real-time RT-PCR process
BMC Bioinformatics 2007, 8:409doi:10.1186/1471-2105-8-409

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.

Array Designer 4.43 – Oligo & cDNA Microarray Design Software

Array Designer 4.43

:: DESCRIPTION

Array Designer designs thousands of primers and probes for oligo and cDNA microarrays in seconds. It designs probes for SNP detection, microarray gene expression and gene expression profiling. In addition, comprehensive support for tiling arrays and resequencing arrays is available.

::DEVELOPER

PREMIER Biosoft

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

Array Designer Demo

:: 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