:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: 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.
:: DESCRIPTION
PolyMarker is an automated bioinformatics pipeline for SNP assay development which increases the probability of generating homoeologue-specific assays for polyploid wheat.
::DEVELOPER
:: SCREENSHOTS
N/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PolyMarker: A fast polyploid primer design pipeline.
Ramirez-Gonzalez RH, Uauy C, Caccamo M.
Bioinformatics. 2015 Feb 2. pii: btv069
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
PrimerZ is a web application dedicated primarily to primer design for genes and human SNPs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: 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.
:: DESCRIPTION
SeqState is a software for primer design and sequence statistics for phylogenetic DNA data sets.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: 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
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: 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.
:: DESCRIPTION
Primer Premier is the most comprehensive software to design and analyze PCR primers.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: 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
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Arányi T, Váradi A, Simon I and Tusnády GE (2006)
The BiSearch web server.
BMC Bioinformatics 7, 431.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: 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.
:: 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
:: 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