Higgins, M, Ravenhall, M, Ward, D, Phelan, J, Ibrahim, A, Forrest, MS, Clark, TG and Campino, S. 2018. PrimedRPA: Primer design for Recombinase polymerase amplification assays. [Online]. BioInformatics. Available from: https://doi.org/10.1093/bioinformatics/bty701
Higgins, M, Ravenhall, M, Ward, D, Phelan, J, Ibrahim, A, Forrest, MS, Clark, TG and Campino, S. PrimedRPA: Primer design for Recombinase polymerase amplification assays [Internet]. BioInformatics; 2018. Available from: https://doi.org/10.1093/bioinformatics/bty701
Higgins, M, Ravenhall, M, Ward, D, Phelan, J, Ibrahim, A, Forrest, MS, Clark, TG and Campino, S (2018). PrimedRPA: Primer design for Recombinase polymerase amplification assays. [Data Collection]. BioInformatics. https://doi.org/10.1093/bioinformatics/bty701
Description
Recombinase polymerase amplification (RPA), an isothermal nucleic acid amplification method, is enhancing our ability to detect a diverse array of pathogens, thereby assisting the diagnosis of infectious diseases and the detection of microorganisms in food and water. However, new bioinformatics tools are needed to automate and improve the design of the primers and probes sets to be used in RPA, particularly to account for the high genetic diversity of circulating pathogens and cross detection of genetically similar organisms. PrimedRPA is a python-based package that automates the creation and filtering of RPA primers and probe sets. It aligns several sequences to identify conserved targets, and filters regions that cross react with possible background organisms.
Data capture method | Experiment |
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Date (Date published in a 3rd party system) | 8 August 2018 |
Language(s) of written materials | English |
Data Creators | Higgins, M, Ravenhall, M, Ward, D, Phelan, J, Ibrahim, A, Forrest, MS, Clark, TG and Campino, S |
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LSHTM Faculty/Department | Faculty of Epidemiology and Population Health > Dept of Infectious Disease Epidemiology Faculty of Infectious and Tropical Diseases > Dept of Pathogen Molecular Biology |
Participating Institutions | London School of Hygiene & Tropical Medicine, London, United Kingdom |
Date Deposited | 28 Aug 2018 11:14 |
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Last Modified | 09 Jul 2021 11:22 |
Publisher | BioInformatics |