Tag: Primer Design

BiSearch 2.69 – Primer Design and Search Tool

BiSearch 2.69

:: 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

BiSearch team

:: 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.

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

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.

CloneAssistant 1.0 – automated Cloning Primer Design

CloneAssistant 1.0

:: DESCRIPTION

CloneAssistant is a standalone software, which can automatically design the cloning primers for users with full consideration of the sequence information of vectors and genes, cloning strategies, the principles of primer design, reading frame, position effects, and enzymatic reaction conditions. It can be used for restriction map analysis, ORF (open reading frame) finding, sequence alignment and complementary analysis, translation, restriction enzyme and universal buffer query, and isocaudamer analysis.

::DEVELOPER

BIS @ Zhejiang University

:: SCREENSHOTS

CloneAssistant

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 CloneAssistant

:: MORE INFORMATION

Citation

J Biotechnol. 2010 Nov;150(3):294-8. doi: 10.1016/j.jbiotec.2010.09.952.
CloneAssistant 1.0: a stand-alone software for automated cloning primer design.
Shao C, Meng Y, Lv S, Zhong W, Wang Z, Chen M.

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

PolyMarker – Fast Polyploid Primer Design Pipeline

PolyMarker

:: DESCRIPTION

PolyMarker is a tool that simplifies the design of genetic markers, a laboratory test to know if certain variant of the genome is present or not in a plant.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

PolyMarker: A fast polyploid primer design pipeline.
Ramirez-Gonzalez RH, Uauy C, Caccamo M.
Bioinformatics. 2015 Jun 15;31(12):2038-9. doi: 10.1093/bioinformatics/btv069.

PolyMarker 0.9.9 – Polyploid Primer Design

PolyMarker 0.9.9

:: 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 Earlham Institute.

:: 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

GLAPD – Whole Genome based LAMP Primer Design for a set of Target Genome

GLAPD

:: DESCRIPTION

GLAPD can design LAMPP(Loop-mediated isothermal amplification) primer sets based on a whole genome. It can also design LAMP primers for a set of target genomes. Users can specify a group of background genomes.

::DEVELOPER

Dr. Chaochun Wei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Bowtie
  • CUDA driver

:: DOWNLOAD

GLAPD

:: MORE INFORMATION

PrimerZ 20171130 – Streamlined Primer design for Promoters, Exons and Human SNPs

PrimerZ 20171130

:: 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.

SeqState 1.4.1 – Primer Design, Sequence Statistics & Indel Coding

SeqState 1.4.1

:: DESCRIPTION

SeqState is a software for primer design and sequence statistics for phylogenetic DNA data sets.

::DEVELOPER

BioInfWeb projects

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

SeqState

:: MORE INFORMATION

Citation

Müller K:
SeqState primer design and sequence statistics for phylogenetic DNA data sets
Applied Bioinformatics 2005, 4:65-69

Müller K
Incorporating information from length-mutational events into phylogenetic analysis.
Molecular Phylogenetics and Evolution 2006, 38:667-676