Tag: Primer Design

Optimus Primer – Primer Design for large-scale Resequencing by Second Generation Sequencing

Optimus Primer

:: DESCRIPTION

Optimus Primer is a PCR enrichment primer design program for next-generation sequencing of human exonic regions.

::DEVELOPER

Laboratory of Guillaume Lettre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Res Notes. 2010 Jul 7;3:185. doi: 10.1186/1756-0500-3-185.
Optimus Primer: A PCR enrichment primer design program for next-generation sequencing of human exonic regions.
Brown AM, Lo KS, Guelpa P, Beaudoin M, Rioux JD, Tardif JC, Phillips MS, Lettre G.

DualPrime 1.1 – Whole-genome Primer Design software

DualPrime 1.1

:: DESCRIPTION

DualPrime selects PCR primers for construction of gene specific tag (GST) microarrays. It tries to minimize the numbers of primers needed to prime all genes of two genomes (or other two lists of genes).

::DEVELOPER

KTH microarray center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • Perl

:: DOWNLOAD

 DualPrime

:: MORE INFORMATION

Citation:

Bioinformatics. 2005 Feb 1;21(3):325-32. Epub 2004 Aug 27.
Dual-genome primer design for construction of DNA microarrays.
Andersson A, Bernander R, Nilsson P.

NoePrimer 3.0 – Primer Design Software

NoePrimer 3.0

:: DESCRIPTION

NoePrimer is designed to specifically meet the growing demand for simplifying increasingly complex primer searches in versatile molecular applications. It makes primer design and analysis so easy with a single mouse click, yet its advanced functions such as multiplex PCR design appeal to demanding needs in the high-throughput research era today.

::DEVELOPER

NoeGen Inc.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

NoePrimer Trial

:: MORE INFORMATION

Order NoePrimer

PrimerPy 0.97a – GUI tool for QPCR Primer Design

PrimerPy 0.97a

:: DESCRIPTION

PrimerPy is a GUI tool for optimal SG QPCR primer design. This branch, Huckleberry, uses “Primer3” as backend engine. The design’s been validated by laboratory experiences; also applicable to conventional PCR.

::DEVELOPER

Suzhao Li

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

 PrimerPy

:: MORE INFORMATION

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.

Primer Prim’er 5.6.0 – PCR Primer Design Tool

Primer Prim’er 5.6.0

:: DESCRIPTION

Primer Prim’er is a PCR primer design tool that completely automates the primer design process.The software generates vector specific PCR primer sets designed to amplify and insert DNA targets into your labs vectors. Primer prim’er is designed to be a powerful tool for structural genomic efforts as well as a teaching tool. Primer prim’er very customizable. Aside from being able to define and employ your own vectors, a variety of settings can be tailored to your needs.

::DEVELOPER

CABM Structural Bioinformatics Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Flash

:: DOWNLOAD

Primer Prim’er

:: MORE INFORMATION

The previously released PERL-CGI version can be found here.

PrimerHunter 1.0.2 – Primer Design for PCR-Based Virus Subtype Identification

PrimerHunter 1.0.2

:: DESCRIPTION

PrimerHunter is a tool for selecting highly sensitive and specific primers for virus subtyping. It takes as input sets of both target and non-target sequences and ensures that selected primers amplify all target sequences and none of the non-target sequences by relying on accurate melting temperature computations based on the nearest-neighbor model of Santalucia and the fractional programming algorithm of  Leber et al.

PrimerHunter Online version

::DEVELOPER

Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

PrimerHunter

:: MORE INFORMATION

Citation:

J. Duitama and D.M. Kumar and E. Hemphill and M. Khan and I.I. Mandoiu and C.E. Nelson,
PrimerHunter: A Primer Design Tool for PCR-Based Virus Subtype Identification,
Nucleic Acids Research 37, pp. 2483-2492, 2009

JCVI Primer Designer 20101122 – High Throughput PCR Primer Design

JCVI Primer Designer 20101122

:: DESCRIPTION

JCVI Primer Designer is the high throughput PCR primer design software that is used at the J. Craig Venter Institute.

::DEVELOPER

the J. Craig Venter Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

JCVI Primer Designer

:: MORE INFORMATION

Citation

Li K, et al. “Novel computational methods for increasing PCR primer design effectiveness in directed sequencing“. BMC Bioinformatics 2008, 9:191.

 

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