PrimedRPA: primer design for recombinase polymerase amplification assays.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
15 02 2019
15 02 2019
Historique:
received:
24
05
2018
revised:
31
07
2018
accepted:
07
08
2018
pubmed:
14
8
2018
medline:
5
11
2019
entrez:
14
8
2018
Statut:
ppublish
Résumé
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. PrimedRPA was implemented in Python 3 and supported on Linux and MacOS and is freely available from http://pathogenseq.lshtm.ac.uk/PrimedRPA.html. Supplementary data are available at Bioinformatics online.
Identifiants
pubmed: 30101342
pii: 5068159
doi: 10.1093/bioinformatics/bty701
pmc: PMC6379019
doi:
Substances chimiques
DNA Primers
0
Recombinases
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
682-684Subventions
Organisme : Medical Research Council
ID : MR/K000551/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/M01360X/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/R020973/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/N010469/1
Pays : United Kingdom
Informations de copyright
© The Author(s) 2018. Published by Oxford University Press.
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