2022-06-03T15:02:17 n14699

Plant virus database (PVirDB)

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This is a custom-built blast database of higher plant viruses and viroids.

A challenge associated with the bioinformatics analysis of sequencing data for diagnostic purposes is the dependency on sequence databases for taxonomic assignment of detection. Although public databases such as the GenBank database maintained at NCBI are the most up to date, the enormous nature of these databases limits their portability across different computing resources. Moreover, sequencing data submitted by users to these public databases may not be accurate, and annotations provided in the GenBank record, such as the taxonomy assignment, which is crucial for accurate diagnosis, may be inaccurate and/or out of data. Additionally, the descriptors of the sequences in the public databases are not harmonized and lack taxonomic information posing an additional challenge to validate sequence homology-based pathogen detections.

Geographical area of data collection

text
Worldwide

Publications

Gauthier M-EA, Lelwala RV, Elliott CE, Windell C, Fiorito S, Dinsdale A, Whattam M, Pattemore J, Barrero RA. Side-by-Side Comparison of Post-Entry Quarantine and High Throughput Sequencing Methods for Virus and Viroid Diagnosis. Biology. 2022; 11(2):263. http://dx.doi.org/10.3390/biology11020263

Research areas

Plant virology
Viroids
Viruses

Cite this collection

Barrero, Roberto; Lelwala, Ruvini; LeBlanc, Zach; Gauthier, Marie-Emilie; (2022): Plant virus database (PVirDB). Queensland University of Technology. (Dataset) https://doi.org/10.25912/RDF_1654232529900

Data file types

The data consists of a .fasta file, which is updated every 3-6 months.

Licence


Creative Commons Attribution 4.0 (CC-BY)
http://creativecommons.org/licenses/by/4.0/

Copyright

© Queensland University of Technology, 2022.

Connections

Has association with
Roberto Barrero Gumiel  (Researcher)

Contacts

Name: Dr Marie-Emilie Gauthier

Other

Date record created:
2022-05-30T09:26:59
Date record modified:
2022-06-03T15:02:17
Record status:
Published - Open Access