scholarly journals Primer Design Assistant (PDA): a web-based primer design tool

2003 ◽  
Vol 31 (13) ◽  
pp. 3751-3754 ◽  
Author(s):  
S.H. Chen
Keyword(s):  
Primer Design ◽  
Design Tool ◽  
Web Based

scholarly journals The web-based multiplex PCR primer design software Ultiplex and the associated experimental workflow: up to 100- plex multiplicity

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jie Yuan ◽  
Ji Yi ◽  
Meixiao Zhan ◽  
Qingqing Xie ◽  
Ting Ting Zhen ◽  
...  
Keyword(s):  
Multiplex Pcr ◽  
Secondary Structures ◽  
Primer Design ◽  
Design Tool ◽  
Web Based ◽  
Tumour Diagnosis ◽  
Design Software ◽  
Nonspecific Amplification ◽  
User Friendly ◽  
Pcr Primer

Abstract Background A large number of variants have been employed in various medical applications, such as providing medication instructions, disease susceptibility testing, paternity testing, and tumour diagnosis. A high multiplicity PCR will outperform other technologies because of its lower cost, reaction time and sample consumption. To conduct a multiplex PCR with higher than 100 plex multiplicity, primers need to be carefully designed to avoid the formation of secondary structures and nonspecific amplification between primers, templates and products. Thus, a user-friendly, highly automated and highly user-defined web-based multiplex PCR primer design software is needed to minimize the work of primer design and experimental verification. Results Ultiplex was developed as a free online multiplex primer design tool with a user-friendly web-based interface (http://ultiplex.igenebook.cn). To evaluate the performance of Ultiplex, 294 out of 295 (99.7%) target primers were successfully designed. A total of 275 targets produced qualified primers after primer filtration, and 271 of those targets were successfully clustered into one compatible PCR group and could be covered by 108 primers. The designed primer group stably detected the rs28934573(C > T) mutation at lower than a 0.25% mutation rate in a series of samples with different ratios of HCT-15 and HaCaT cell line DNA. Conclusion Ultiplex is a web-based multiplex PCR primer tool that has several functions, including batch design and compatibility checking for the exclusion of mutual secondary structures and mutual false alignments across the whole genome. It offers flexible arguments for users to define their own references, primer Tm values, product lengths, plex numbers and tag oligos. With its user-friendly reports and web-based interface, Ultiplex will provide assistance for biological applications and research involving genomic variants.

scholarly journals The Narrative Event Diagram

2009 ◽  
pp. 101-118
Author(s):  
Helyn Gould ◽  
Michael Hughes ◽  
Paul Maharg ◽  
Emma Nicol
Keyword(s):  
Professional Learning ◽  
Information Science ◽  
Further Education ◽  
Design Tool ◽  
Design History ◽  
Game Based Learning ◽  
Web Based ◽  
Design Iteration ◽  
The United Kingdom ◽  
Narrative Event

Game-based learning and simulation is a powerful mode of learning, used by industries as diverse as aviation and health sciences. While there are many generic Virtual Learning Environments available to further education and higher education in the United Kingdom, there is no widely available open-source Web-based simulation environment for professional learning. The SIMPLE (SIMulated Professional Learning Environment) project has designed, created, implemented and is in the process of evaluating such an environment in a range of disciplinary settings. The simulations that are being created place both undergraduates and postgraduates in a professional context where their work is, as it will be in the workplace, distributed between tools, colleagues, resources, anticipated, and unanticipated problems. One of the key tools that staff will use to create simulations is the “narrative event diagram”, a design tool as well as a means by which the narrative of the simulation is constructed. This chapter will describe the tool, its design history and context, its current use, and next design iteration. In particular it will show the interdisciplinary genesis of the tool’s design, arising from the confluence of computer science, information science, and narrative theory, and its power in designing professional educational simulations.

Primer Prim’r: A web based server for automated primer design

2004 ◽  
Vol 5 (1/2) ◽  
pp. 13-21 ◽  
Author(s):  
John K. Everett ◽  
Thomas B. Acton ◽  
Gaetano T. Montelione
Keyword(s):  
Primer Design ◽  
Web Based

Web-Based Cad Tools for a Networked Manufacturing Service

1998 ◽  
Author(s):  
Fu-Chung F. Wang ◽  
Paul K. Wright
Keyword(s):  
New Product Development ◽  
Design Tool ◽  
Internet Technology ◽  
Machining Process ◽  
Global Network ◽  
The Internet ◽  
Distributed Design ◽  
Cad Tools ◽  
Web Based ◽  
Design And Manufacturing

Abstract New techniques in Information Technology are now changing not only our daily life, but also the professional practice of product design and manufacturing for new product development. Internet technology in particular opens up another domain for building future CAD/CAM environments. This environment will be a global, network-centric environment with various members providing different software tools, manufacturing facilities, and analysis services for distributed design and fabrication. In this paper, we first briefly describe a vision and current development in a distributed design and manufacturing environment. The paper then emphasizes how current CAD tools will evolve to facilitate the distributed design and fabrication process. In particular, the development of a set of Web-based design tools for fabricating parts using a machining process via the Internet is presented. Experiments on machining 2-1/2 D and freeform parts through this Java-based design tool have shown the feasibility for a networked machining service via the Internet.

scholarly journals MDC-Analyzer: A novel degenerate primer design tool for the construction of intelligent mutagenesis libraries with contiguous sites

BioTechniques ◽  
2014 ◽  
Vol 56 (6) ◽  
Author(s):  
Lixia Tang ◽  
Xiong Wang ◽  
Beibei Ru ◽  
Hengfei Sun ◽  
Jian Huang ◽  
...  
Keyword(s):  
Primer Design ◽  
Design Tool ◽  
Degenerate Primer

scholarly journals URPD: a specific product primer design tool

2012 ◽  
Vol 5 (1) ◽  
pp. 306 ◽  
Author(s):  
Li-Yeh Chuang ◽  
Yu-Huei Cheng ◽  
Cheng-Hong Yang
Keyword(s):  
Primer Design ◽  
Design Tool ◽  
Specific Product

scholarly journals PAVOOC: Designing CRISPR sgRNAs using 3D protein structures and functional domain annotation

2018 ◽  
Author(s):  
Moritz Schaefer ◽  
Dr. Djork-Arné Clevert ◽  
Dr. Bertram Weiss ◽  
Dr. Andreas Steffen
Keyword(s):  
Gene Editing ◽  
State Of The Art ◽  
Protein Structures ◽  
Design Tool ◽  
Protein Crystal ◽  
Functional Domain ◽  
Web Based ◽  
Domain Annotation ◽  
Sgrna Design ◽  
Processing Steps

AbstractSummary: sgRNAs targeting the same gene can significantly vary in terms of efficacy and specificity. PAVOOC (Prediction And Visualization of On- and Off-targets for CRISPR) is a web-based CRISPR sgRNA design tool that employs state-of-the art machine learning models to prioritize most effective candidate sgRNAs. In contrast to other tools, it maps sgRNAs to functional domains and protein structures and visualizes cut sites on corresponding protein crystal structures. Furthermore, PAVOOC supports HDR template generation for gene editing experiments and the visualization of the mutated amino acids in 3D.Availability and Implementation: PAVOOC is available under https://pavooc.me and accessible using current browsers (Chrome/Chromium recommended). The source code is hosted at github.com/moritzschaefer/pavooc under the MIT License. The backend, including data processing steps, and the frontend is implemented in Python 3 and ReactJS respectively. All components run in a simple Docker environment.Contact: [email protected]

A web-based adaptive tutor to teach PCR primer design

2011 ◽  
Vol 40 (1) ◽  
pp. 8-13 ◽  
Author(s):  
Janneke R. van Seters ◽  
Joan Wellink ◽  
Johannes Tramper ◽  
Martin J. Goedhart ◽  
Miriam A. Ossevoort
Keyword(s):  
Primer Design ◽  
Web Based ◽  
Pcr Primer

scholarly journals MSP-HTPrimer: a high-throughput primer design tool to improve assay design for DNA methylation analysis in epigenetics

2016 ◽  
Vol 8 (1) ◽  
Author(s):  
Ram Vinay Pandey ◽  
Walter Pulverer ◽  
Rainer Kallmeyer ◽  
Gabriel Beikircher ◽  
Stephan Pabinger ◽  
...  
Keyword(s):  
Dna Methylation ◽  
High Throughput ◽  
Primer Design ◽  
Design Tool ◽  
Methylation Analysis ◽  
Assay Design ◽  
Dna Methylation Analysis
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