Tag: PCR

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

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.

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

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

PCRduplicates – Estimate PCR Duplication Rate from High-throughput Sequencing data

PCRduplicates

:: DESCRIPTION

PCRduplicates is a computational method to estimate the PCR duplication rate in high-throughput DNA sequencing experiments

::DEVELOPER

Bansal Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

PCRduplicates

:: MORE INFORMATION

Citation

Bansal V.
A computational method for estimating the PCR duplication rate in DNA and RNA-seq experiments.
BMC Bioinformatics. 2017 Mar 14;18(Suppl 3):43. doi: 10.1186/s12859-017-1471-9. PMID: 28361665; PMCID: PMC5374682.

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.

MPprimer 1.5 – Reliable Multiplex PCR Primer Design

MPprimer 1.5

:: DESCRIPTION

MPprimer: a program for reliable multiplex PCR primer design. MPprimer employs the widely used primer design program Primer3 [Rozen, et al. 2000] and the primer specificity evaluation program MFEprimer [Qu, et al. 2009] to design and evaluate the candidate primers based on genomic or transcript DNA database, followed by careful examination to avoid primer dimerization. The graph-expanding algorithm derived from the greedy algorithm was used to determine the optimal primer set combinations (PSCs) for multiplex PCR. In addition, MPprimer provides a virtual electrophotogram to help users choose the best PSC. In short, MPprimer is a valuable tool for designing specific, no dimer formation and amplicons size constrained PSCs to improve the multiplex PCR experiments.

::DEVELOPER

MPprimer team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs

:: DOWNLOAD

 MPprimer

:: MORE INFORMATION

Citation:

Zhiyong Shen, Wubin Qu, Wen Wang, Yiming Lu, Yonghong Wu, Zhifeng Li, Xingyi Hang, Xiaolei Wang, Dongsheng Zhao, Chenggang Zhang.
MPprimer: a program for reliable multiplex PCR primer design.
BMC Bioinformatics, 2010, 11:143

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

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