Tag: Primer Design

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.

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.

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, MutantChecker , PCR 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.

PrimerDesign-M – Multiple-alignment based Multiple-primer Design tool

PrimerDesign-M

:: DESCRIPTION

PrimerDesign-M was developed to meet the demands of primer design for highly variable sets of aligned sequences. It includes design requirements for next-generation sequences (NGS) including 454 sequences. It can also be used for primer and probe design for PCR, Sanger sequencing, and other systems with custom barcodes and DNA handles for universal primer annealing. The tool will design several alternative primer sets, whenever possible.

::DEVELOPER

PrimerDesign-M team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PrimerDesign-M: a multiple-alignment based multiple-primer design tool for walking across variable genomes.
Yoon H, Leitner T.
Bioinformatics. 2014 Dec 17. pii: btu832.

Primegens 2.0.5 – Primer Design for Microarray

Primegens 2.0.5

:: DESCRIPTION

Primegens ((PRIMEr Design Using GEN Specific Fragments) is a software for high-throughput primer and probe design. The program uses two third party executables like Primer3 and Megablast.

::DEVELOPER

Primegens Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows

:: DOWNLOAD

 Primegens

:: MORE INFORMATION

Citation

Gyan Prakash Srivastava, Juyuan Guo, Huidong Shi and Dong Xu.
” PRIMEGENS-v2: genome-wide primer design for analyzing DNA methylation pattern of CpG island“.
Bioinformatics 2008 24(17):1837-42.

3PD – Primer design for Chromosome Conformation Capture Assays

3PD

:: DESCRIPTION

3PD is a bioinformatics solution  to support the experimentalist in detecting long-ranging intra or inter chromosomal contacts by Chromosome conformation capture (3C) assays.

::DEVELOPER

Dieterich lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Genomics. 2009 Dec 29;10:635. doi: 10.1186/1471-2164-10-635.
3PD: Rapid design of optimal primers for chromosome conformation capture assays.
Fröhler S, Dieterich C.