HTP-OligoDesigner – An Online Primer Design Tool

HTP-OligoDesigner

:: DESCRIPTION

HTP-OligoDesigner was created to provide the scientific community with a simple and intuitive online primer design tool for both laboratory-scale and high-throughput projects of sequence-independent gene cloning and site-directed mutagenesis and a Tm calculator for quick queries.

:: DEVELOPER

HTP-OligoDesigner team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

J Comput Biol. 2016 Jan;23(1):27-9. doi: 10.1089/cmb.2015.0148. Epub 2015 Nov 5.
HTP-OligoDesigner: An Online Primer Design Tool for High-Throughput Gene Cloning and Site-Directed Mutagenesis.
Camilo CM, Lima GM, Maluf FV, Guido RV, Polikarpov I.

PolyMarker 0.7.3 – Polyploid Primer Design

PolyMarker 0.7.3

:: DESCRIPTION

PolyMarker is an automated bioinformatics pipeline for SNP assay development which increases the probability of generating homoeologue-specific assays for polyploid wheat.

::DEVELOPER

The Genome Analysis Centre (TGAC)

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux
  • BioRuby

:: DOWNLOAD

 PolyMarker

:: MORE INFORMATION

Citation

PolyMarker: A fast polyploid primer design pipeline.
Ramirez-Gonzalez RH, Uauy C, Caccamo M.
Bioinformatics. 2015 Feb 2. pii: btv069

Primer Premier 6.23 – PCR Primer Design Software

Primer Premier 6.23

:: DESCRIPTION

Primer Premier is the most comprehensive software to design and analyze PCR primers.

::DEVELOPER

PREMIER Biosoft

:: SCREENSHOTS

:: REQUIREMENTS

  • MacOsX / Windows

:: DOWNLOAD

Primer Premier Demo

:: MORE INFORMATION

BiSearch 2.47 – Primer Design and Search Tool

BiSearch 2.47

:: DESCRIPTION

BiSearch is a primer-design algorithm for DNA sequences. It may be used for both bisulfite converted as well as for original not modified sequences. You can search various genomes with the designed primers to avoid non-specific PCR products by our fast ePCR method. This is especially recommended when primers are designed to amplify the highly redundant bisulfite treated sequences.

::DEVELOPER

the Institute of Enzymology, Hungarian Academy of Sciences.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Arányi T, Váradi A, Simon I and Tusnády GE (2006)
The BiSearch web server.
BMC Bioinformatics 7, 431.

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

3PD team

:: 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.

MPRIMER – High-throughput Multiplex PCR Primer Design

MPRIMER

:: DESCRIPTION

MPRIMER is a reliable, flexible and high-throughput multiplex PCR primer design software. It i) utilizes the famous Primer3 program to select candidate primers; ii) uses thermodynamics to measure the stability of misprimer and dimers; iii) implements k-mer index algorithm to fast check the specificity against large genome database; iv) designs a flexible plugin mechanism for easily extending the applications; v) has a self-learning system to redesign primers when primers are incompatible; vi) can auto-group the incompatible templates into different tubes; vii) is suitable for high-throughput primer design.

::DEVELOPER

CZlab @ Beijing Institute of Radiation Medcine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: 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

Primegens w3 – Primer Design for Microarray

Primegens w3

:: 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.

Primerize 1.0 – PCR Assembly Primer Design

Primerize 1.0

:: DESCRIPTION

Primerize is a Web Server for primer designs of DNA sequence PCR assembly. Primerize is optimized to reduce primer boundaries mispriming, is designed for fixed sequences of RNA problems, and passed wide and stringent tests.

::DEVELOPER

DAS lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 Primerize

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2015 May 20. pii: gkv538.
Primerize: automated primer assembly for transcribing non-coding RNA domains.
Tian S, Yesselman JD, Cordero P, Das R

PrimerZ – Streamlined Primer design for Promoters, Exons and Human SNPs

PrimerZ 20150216

:: DESCRIPTION

PrimerZ is a web application dedicated primarily to primer design for genes and human SNPs.

::DEVELOPER

PrimerZ team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PrimerZ: streamlined primer design for promoters, exons and human SNPs.
Tsai MF, Lin YJ, Cheng YC, Lee KH, Huang CC, Chen YT, Yao A.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W63-5. Epub 2007 May 30.

GA-CTPP – Confronting Two-pair Primers Design Using Genetic Algorithm

GA-CTPP

:: DESCRIPTION

GA-CTPP is a GA (genetic algorithm)-based method to design a feasible CTPP primer set for performing a reliable PCR experiment.

::DEVELOPER

GA-CTPP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Oct 13;11:509. doi: 10.1186/1471-2105-11-509.
Confronting two-pair primer design for enzyme-free SNP genotyping based on a genetic algorithm.
Yang CH1, Cheng YH, Chuang LY, Chang HW.