UniPrime2 2.10 – Universal Primer Design Server

UniPrime2 2.10

:: DESCRIPTION

UniPrime2 is an experimentally validated, fully automated program that generates successful cross-species primers that take into account the biological aspects of the PCR. UniPrime2 automatically retrieves and aligns orthologous sequences from GenBank, identifies regions of conservation within the alignment and generates suitable primers that can amplify variable genomic regions. UniPrime2 differs from previous automatic primer design programs in that all steps of primer design are automated, saved and are phylogenetically limited. We have experimentally verified the efficiency and success of this program.

::DEVELOPER

UniPrime2 team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 UniPrime2

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W209-13. Epub 2009 Apr 28.
UniPrime2: a web service providing easier Universal Primer design.
Boutros R, Stokes N, Bekaert M, Teeling EC.

AutoDimer 1.0 – Screening Tool for Primer-dimer & Hairpin Structures

AutoDimer 1.0

:: DESCRIPTION

AutoDimer software was developed to rapidly screen previously selected PCR primers for primer-dimer and hairpin interactions in short DNA oligomers (< 30 nucleotides). AutoDimer was originally created to assist in the development of multiplex PCR assays for probing STR and SNP markers for forensic purposes.

::DEVELOPER

Peter M. Vallone

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

AutoDimer

:: MORE INFORMATION

Citation

Vallone, P.M. and Butler, J.M. (2004)
AutoDimer: a screening tool for primer-dimer and hairpin structures.
Biotechniques, 37(2): 226-231.

DefiningTheRain – Automatically analysing BioRad’s Digital Droplet PCR Output

DefiningTheRain

:: DESCRIPTION

Defining The Rain is a javascript program that allows user to cluster digital droplet PCR data to define cut offs and improve calling

::DEVELOPER

DefiningTheRain team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • javascript

:: DOWNLOAD

  DefiningTheRain

:: MORE INFORMATION

Citation

Low copy target detection by Droplet Digital PCR through application of a novel open access bioinformatic pipeline, ‘definetherain’.
Jones M, Williams J, G?rtner K, Phillips R, Hurst J, Frater J.
J Virol Methods. 2014 Jun;202:46-53. doi: 10.1016/j.jviromet.2014.02.020.

GenoFrag 2.1 – Design Primers Optimized for Whole Genome Scanning by Long-range PCR Amplification

GenoFrag 2.1

:: DESCRIPTION

GenoFrag was developed for the analysis of Staphylococcus aureus genome plasticity by whole genome amplification in ~10 kb‐long fragments. A set of primers was generated from the genome sequence of S.aureus N315, employed here as a reference strain. Two subsets of primers were successfully used to amplify two portions of the N315 chromosome. This experimental validation demonstrates that GenoFrag is a robust and reliable tool for primer design and that whole genome PCR scanning can be envisaged for the analysis of genome diversity in S.aureus, one of the major public health concerns worldwide.

::DEVELOPER

GenoFrag Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/Unix/MacOsX
  • Python

:: DOWNLOAD

 GenoFrag Source Code

:: MORE INFORMATION

Citation

Nouri Ben Zakour et. al.
GenoFrag: software to design primers optimized for whole genome scanning by long‐range PCR amplification
Nucl. Acids Res. (2004) 32 (1): 17-24

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

GenEx 7.0 – Analyze Real-time qPCR Data

GenEx 7.0

:: DESCRIPTION

GenEx is a popular software for qPCR data processing and analysis. Built in a modular fashion GenEx provides a multitude of functionalities for the qPCR community, ranging from basic data editing and management to advanced cutting-edge data analysis.

::DEVELOPER

MultiD Analyses AB

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  GenEx

:: MORE INFORMATION

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

AlleleID 7.85 – Assay Design for Bacterial Identification

AlleleID 7.85

:: DESCRIPTION

AlleleID® is a comprehensive desktop tool designed to address the challenges of bacterial identification, pathogen detection or species identification. With ClustalW multiple sequence alignment at its core, AlleleID® can be used to design species identification/cross species probes for microarrays or real time PCR including SYBR® Green, TaqMan® MGB, TaqMan® probes, Molecular Beacons and real time PCR primers. AlleleID® also offers support for designing microarray experiments for detecting alternative splicing events.

::DEVELOPER

PREMIER Biosoft

:: SCREENSHOTS

:: REQUIREMENTS

  • MacOsX / Windows

:: DOWNLOAD

AlleleID 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

AAScan 2.2 / MutantChecker 1.3 / PCR Cloning 1.5 – Primer Design and Sequence Analysis for High-throughput Scanning Mutagenesis

AAScan 2.2 / MutantChecker 1.3 / PCR Cloning 1.5

:: DESCRIPTION

AAscan, PCRdesign and MutantChecker is a suite of programs for primer design and sequence analysis for high-throughput scanning mutagenesis.

AAScan (formely AlaScan) – batch primer design software for scanning mutagenesis
MutantChecker – helps to analyse the sequenceing results from scanning mutagenesis
PCR Cloning – design of primers for ligation-independent cloning

::DEVELOPER

Laboratory of Biomolecular Research (LBR)

:: SCREENSHOTS

aascan

MutantChecker

PCRCloning

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 AAScan, MutantCheckerPCR Cloning

:: MORE INFORMATION

Citation

PLoS One. 2013 Oct 30;8(10):e78878. doi: 10.1371/journal.pone.0078878. eCollection 2013.
AAscan, PCRdesign and MutantChecker: a suite of programs for primer design and sequence analysis for high-throughput scanning mutagenesis.
Sun D1, Ostermaier MK, Heydenreich FM, Mayer D, Jaussi R, Standfuss J, Veprintsev DB.