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MRPrimerV: a database of PCR primers for RNA virus detection

Title
MRPrimerV: a database of PCR primers for RNA virus detection
Authors
Kim, HyerinKang, NaNaAn, KyuHyeonKim, DoyunKoo, JaeHyungKim, Min-Soo
DGIST Authors
Kim, Hyerin; Kang, NaNa; An, KyuHyeon; Kim, Doyun; Koo, JaeHyungKim, Min-Soo
Issue Date
2017-01-04
Citation
Nucleic Acids Research, 45(D1), D475-D481
Type
Article
Article Type
Article
Keywords
Databases, Nucleic AcidDesignDNA PrimersDNAprimer DNAGeneticsHumanHumansNucleic Acid DatabasePolymerase Chain ReactionPolymerase Chain ReactionProbe DatabaseReal Time PCRResourceRNA VirusRNA VirusesRTPrimerDBUpdateVirologyVirus Diseases
ISSN
0305-1048
Abstract
Many infectious diseases are caused by viral infections, and in particular by RNA viruses such as MERS, Ebola and Zika. To understand viral disease, detection and identification of these viruses are essential. Although PCR is widely used for rapid virus identification due to its low cost and high sensitivity and specificity, very few online database resources have compiled PCR primers for RNA viruses. To effectively detect viruses, the MRPrimerV database (http://MRPrimerV.com) contains 152 380 247 PCR primer pairs for detection of 1818 viruses, covering 7144 coding sequences (CDSs), representing 100% of the RNA viruses in the most up-to-date NCBI RefSeq database. Due to rigorous similarity testing against all human and viral sequences, every primer in MRPrimerV is highly target-specific. Because MRPrimerV ranks CDSs by the penalty scores of their best primer, users need only use the first primer pair for a single-phase PCR or the first two primer pairs for two-phase PCR. Moreover, MRPrimerV provides the list of genome neighbors that can be detected using each primer pair, covering 22 192 variants of 532 RefSeq RNA viruses. We believe that the public availability of MRPrimerV will facilitate viral metagenomics studies aimed at evaluating the variability of viruses, as well as other scientific tasks. © 2016 The Author(s).
URI
http://hdl.handle.net/20.500.11750/4248
DOI
10.1093/nar/gkw1095
Publisher
Oxford University Press
Related Researcher
Files:
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Collection:
Brain and Cognitive SciencesThe Koo Lab - ChemoReception Laboratory(CRLab)1. Journal Articles


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