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The Subviral RNA Database: A Toolbox for Viroids, the Hepatitis Delta Virus and Satellite RNAs Research

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The Subviral RNA Database: A Toolbox for Viroids, the Hepatitis Delta Virus and Satellite RNAs Research

Lynda Rocheleau et al. BMC Microbiol.

Abstract

Background: Viroids, satellite RNAs, satellites viruses and the human hepatitis delta virus form the 'brotherhood' of the smallest known infectious RNA agents, known as the subviral RNAs. For most of these species, it is generally accepted that characteristics such as cell movement, replication, host specificity and pathogenicity are encoded in their RNA sequences and their resulting RNA structures. Although many sequences are indexed in publicly available databases, these sequence annotation databases do not provide the advanced searches and data manipulation capability for identifying and characterizing subviral RNA motifs.

Description: The Subviral RNA database is a web-based environment that facilitates the research and analysis of viroids, satellite RNAs, satellites viruses, the human hepatitis delta virus, and related RNA sequences. It integrates a large number of Subviral RNA sequences, their respective RNA motifs, analysis tools, related publication links and additional pertinent information (ex. links, conferences, announcements), allowing users to efficiently retrieve and analyze relevant information about these small RNA agents.

Conclusion: With its design, the Subviral RNA Database could be considered as a fundamental building block for the study of these related RNAs. It is freely available via a web browser at the URL: http://subviral.med.uottawa.ca.

Figures

Figure 1
Figure 1
Organization of the Subviral RNA Database. Sections related to sequence data, new contents, announcements, conferences, links, bioinformatics tools and Subviral RNA motifs can be accessed directly using buttons located at the left side.
Figure 2
Figure 2
Overview of the different RNA motifs associated with the indexed Subviral RNA species. Users have access to information on various RNA motifs found in subviral RNA agents. A) Type III hammerhead ribozyme; B) delta ribozyme; C) hairpin ribozyme; and D) RY motif. Important nucleotides for each RNA motif are colored.
Figure 3
Figure 3
Analysis of the 260 RY motifs indexed in the Subviral RNA database. A) Structural representation of the primary sequences of the RY motifs. B) Consensus secondary structure derived from the analysis of natural variants of the RY motifs. Greater that 99% conserved nucleotides are indicated in red, base-pairs conserved through covariations are indicated by blue ovals, and IUPAC 1-letter code abbreviations are used for the identity of the non-conserved nucleotides on the secondary structure (B: U/C/G, D: A/U/G, H: A/U/C, K: U/G, N: A/C/G/U, R: A/G, V: A/C/G, Y: C/U). C) Logo representation of the sequence conservation of the RY motifs [8]. Greater that 99% conserved nucleotides are indicated in red.

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