Category: PCR / Primer Design

LinRegPCR 20210614 – Analysis of Quantitative PCR Data

LinRegPCR 20210614

:: DESCRIPTION

LinRegPCR is a program for the analysis of quantitative RT-PCR (qPCR) data resulting from monitoring the PCR reaction with SYBR green or similar fluorescent dyes. The program determines a baseline fluorescence and does a baseline subtraction. Then a Window-of-Linearity is set and PCR efficiencies per sample are calculated. With the mean PCR efficiency per amplicon, the Ct value per sample and the fluorescence threshold set to determnine the Ct, the starting concentration per sample, expressed in arbitrary fluorescence units, is calculated

::DEVELOPER

J. M. Ruijter, S. van der Velden,A. Ilgun @ Heart Failure Research Center (HFRC)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Microsoft Excel

:: DOWNLOAD

 LinRegPCR

:: MORE INFORMATION

Citation

Ramakers C, Ruijter JM, Deprez RH, Moorman AF. (2003)
Assumption-free analysis of quantitative real-time PCR data
Neurosci Lett 2003 Mar 13;339(1): 62-66

PerlPrimer 1.1.21 – Open-source PCR Primer Design

PerlPrimer 1.1.21

:: DESCRIPTION

PerlPrimer is a free, open-source GUI application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing. It aims to automate and simplify the process of primer design.

::DEVELOPER

Owen Marshall at Murdoch Childrens Research Institute

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

PerlPrimer

:: MORE INFORMATION

Citation

Owen J. Marshall
PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR
Bioinformatics (2004) 20 (15): 2471-2472.

BatchPrimer3 1.0 – High Throughput Web Application for PCR and Sequencing Primer Design

BatchPrimer3 1.0

:: DESCRIPTION

BatchPrimer3 is a comprehensive web primer design program using Primer3 core program as a major primer design engine to design different types of PCR primers and sequencing primers in a high-through manner. BatchPrimer3 allows users to design several types of primers including generic primers, hybridization oligos, SSR primers together with SSR detection, and SNP genotyping primers (including single-base extension primers, allele-specific primers, and tetra-primers for tetra-primer ARMS PCR), as well as DNA sequencing primers. A batch input of large number of sequences and a tab-delimited result output greatly facilitates rapid primer design and ordering process.

::DEVELOPER

Department of Plant Sciences, University of California

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

BatchPrimer3: a high throughput web application for PCR and sequencing primer design.
You FM, Huo N, Gu YQ, Luo MC, Ma Y, Hane D, Lazo GR, Dvorak J, Anderson OD.
BMC Bioinformatics. 2008 May 29;9:253.

RJPrimers 1.0 – Transposable Element Junction based PCR Primer Design

RJPrimers 1.0

:: DESCRIPTION

RJPrimers is a high-throughput software tool to identify unique repeat junction and design TE-based primers for high-throughput marker development. This tool first identifies potentially unique repeat junctions using BLAST against fully annotated repeat databases and a repeat junction finding algorithm, and then designs TE based primers using Primer3 and BatchPrimer3.

::DEVELOPER

GrainGenes

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Frank M. You, Humphrey Wanjugi, Naxin Huo, Gerard R. Lazo, Ming-Cheng Luo, Olin D. Anderson, Jan Dvorak and Yong Q. Gu.
RJPrimers: unique transposable element insertion junction discovery and PCR primer design for marker development.
Nucl. Acids Res. (2010) 38 (suppl 2): W313-W320. doi:10.1093/nar/gkq425

CutSPR – Construction of Mutagenesis Vector based on the pJoe8999 plasmid system

CutSPR

:: DESCRIPTION

CutSPR is a bioinformatic tool for rapid primer design, and facilitates the cloning of specific CRISPR-Cas9-based mutagenesis plasmids.

::DEVELOPER

Göttingen Genomics Laboratory, Institut für Mikrobiologie and Genetik

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOs
  • Python

:: DOWNLOAD

CutSPR

:: MORE INFORMATION

Citation

Schilling T, Dietrich S, Hoppert M, Hertel R.
A CRISPR-Cas9-Based Toolkit for Fast and Precise In Vivo Genetic Engineering of Bacillus subtilis Phages.
Viruses. 2018 May 4;10(5):241. doi: 10.3390/v10050241. PMID: 29734705; PMCID: PMC5977234.

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

:: 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

PrimerStation – Multiplex PCR Primer Design site

PrimerStation

:: DESCRIPTION

PrimerStation is a web service to calculate optimal primer sets that are guaranteed high specificity against whole human genome.

::DEVELOPER

Morishita Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W665-9.
PrimerStation: a highly specific multiplex genomic PCR primer design server for the human genome.
Yamada T, Soma H, Morishita S.

PD5 1.5 – Software Library for the Development of Primer Design Applications

PD5 1.5

:: DESCRIPTION

PD5 is a C++ software library of classes for the design and analysis of primers suitable for a wide range of PCR applications.

PD5 Online Version

::DEVELOPER

 the Bioinformatics group in the Department of Computer Science at Aberystwyth University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOSX / Linux
  • C++ Compiler

:: DOWNLOAD

 PD5

:: MORE INFORMATION

Citation

PLoS One. 2013 Nov 21;8(11):e80156. doi: 10.1371/journal.pone.0080156.
PD5: A General Purpose Library for Primer Design Software.
Riley MC, Aubrey W, Young M, Clare A.

Oligo Heat Map 1.52 – Check Thermodynamical Parameters for PCR primers

Oligo Heat Map 1.52

:: DESCRIPTION

OligoHeatMap (OHM) is a web-application for checking thermodynamical parameters for PCR primers and computing graphical representation to show specificity of target sequences .

::DEVELOPER

Olivier Croce

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Javascript
  • Php

:: DOWNLOAD

    Oligo Heat Map

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W154-6. Epub 2008 Apr 25.
OligoHeatMap (OHM): an online tool to estimate and display hybridizations of oligonucleotides onto DNA sequences.
Croce O, Chevenet F, Christen R.