Efforts were initiated to refine RVDB from version 19.0. This included removal of misannotated sequences and sequences determined to be irrelevant for virus detection in RVDB. This is indicated in the Release Notes and the list of removed accession numbers is included in the Annotation sheet.
Reference Viral Database (RVDB) is developed by Arifa Khan's group at CBER, FDA for enhancing virus detection using next-generation sequencing (NGS) technologies. RVDB is available as Unclustered (U-) and Clustered (C-) nucleotide sequence files. The scripts and steps involved in generating and updating RVDB have been assembled into a pipeline (reported in mSphere) and is available with instructions at GitHub.
The SQLite form of U-RVDB is provided using the sqlite3 module available in python, as described by GitHub. From version 15.1 and thereafter, the RVDB SQLiteDB is converted to SQL to provide a flexible import format.
A proteic version of RVDB, was developed by Marc Eloit’s group at Institut Pasteur (RVDB-prot and RVDB-prot-HMM). The proteic RVDB may be used to complement analysis using these nucleotidic databases.
Unclustered (U-) nucleotide sequence files.
Clustered (C-) nucleotide sequence files.
|RVDB Version (Release date)||Sequence files in FASTA format||Release notes in plain text file|
|Current Release v20.0 (Sept, 3 2020)||C-RVDBv20.0.fasta||C-RVDBv20.0.release notes|
|v19.0 (Jun 29, 2020)||C-RVDBv19.0.fasta||C-RVDBv19.0.release notes|
|v18.0 (Mar 2, 2020)||C-RVDBv18.0.fasta||C-RVDBv18.0.release notes|
|v17.0 (Nov 6, 2019)||C-RVDBv17.0.fasta||C-RVDBv17.0.release notes|
|v16.0 (May 29, 2019)||C-RVDBv16.0.fasta||C-RVDBv16.0.release notes|
|v15.1 (Feb 6, 2019)||C-RVDBv15.1.fasta||C-RVDBv15.1.release notes|
|v14.0 (Oct 1, 2018)||C-RVDBv14.0.fasta||C-RVDBv14.0.release notes|
|v13.0 (Jun 11, 2018)||C-RVDBv13.0.fasta||C-RVDBv13.0.release notes|
|v12.2 (Feb 12, 2018)||C-RVDBv12.2.fasta||C-RVDBv12.2.release notes|
|v11.5 (Sept 27, 2017)||C-RVDBv11.5.fasta||C-RVDBv11.5.release notes|
|v11.3 (Aug 1, 2017)||C-RVDBv11.3.fasta||C-RVDBv11.3.release notes|
|v10.2 (U-May 5, 2017; C-Dec. 28, 2016)||C-RVDBv10.2.fasta||C-RVDBv10.2.release notes|
Goodacre N, Aljanahi A, Nandakumar S, Mikailov M, Khan AS. A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection. mSphere. 2018 Mar 14;3(2). pii: e00069-18. doi: 10.1128/mSphereDirect.00069-18. eCollection 2018 Mar-Apr. PubMed PMID: 29564396; PubMed Central PMCID: PMC5853486.
If you have any questions or comments regarding RVDB nucleotidic databases, please contact Arifa Khan (Arifa.Khan@fda.hhs.gov). If you have any technical questions or comments regarding the website, please contact the Bioinformatics Core at University of Delaware firstname.lastname@example.org.