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.

NormFinder 0.953 – Normalization of Real-Time Quantitative Reverse Transcription-PCR Data

NormFinder 0.953

:: DESCRIPTION

NormFinder is an algorithm for identifying the optimal normalization gene among a set of candidates.It ranks the set of candidate normalization genes according to their expression stability in a given sample set and given experimental design.NormFinder can analyze expression data obtained through any quantitative method e.g. real time RT-PCR and microarray based expression analysis.

::DEVELOPER

Department of Molecular MedicineAarhus University Hospital

:: SCREENSHOTS

:: REQUIREMENTS

  • Excel / R package

:: DOWNLOAD

 NormFinder

:: MORE INFORMATION

Citation

C.L., Ledet-Jensen J., Ørntoft T.
Normalization of real-time quantitative RT-PCR data: a model based variance estimation approach to identify genes suited for normalization – applied to bladder- and colon-cancer data-sets.
Cancer Research. 2004 (64): 5245-5250

OligoCalc 3.26 – Oligonucleotide Properties Calculator

OligoCalc 3.26

:: DESCRIPTION

OligoCalc is a web-accessible, client-based computational engine for reporting DNA and RNA single-stranded and double-stranded properties, including molecular weight, solution concentration, melting temperature, estimated absorbance coefficients, inter-molecular self-complementarity estimation and intra-molecular hairpin loop formation.

::DEVELOPER

Warren A. Kibbe, Ph.D.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

 OligoCalc

:: MORE INFORMATION

Citation

Kibbe WA.
OligoCalc: an online oligonucleotide properties calculator‘. (2007)
Nucleic Acids Res. 35(webserver issue): May 25.