A database of flavivirus RNA structures with a search algorithm for pseudoknots and triple base interactions

Bioinformatics, vol. 37, pp. 956–962

Abstract

MOTIVATION: The Flavivirus genus includes several important pathogens, such as Zika, dengue and yellow fever virus. Flavivirus RNA genomes contain a number of functionally important structures in their 3' untranslated regions (3'UTRs). Due to the diversity of sequences and topologies of these structures, their identification is often difficult. In contrast, predictions of such structures are important for understanding of flavivirus replication cycles and development of antiviral strategies. RESULTS: We have developed an algorithm for structured pattern search in RNA sequences, including secondary structures, pseudoknots and triple base interactions. Using the data on known conserved flavivirus 3'UTR structures, we constructed structural descriptors which covered the diversity of patterns in these motifs. The descriptors and the search algorithm were used for the construction of a database of flavivirus 3'UTR structures. Validating this approach, we identified a number of domains matching a general pattern of exoribonuclease Xrn1-resistant RNAs in the growing group of insect-specific flaviviruses. AVAILABILITY AND IMPLEMENTATION: The Leiden Flavivirus RNA Structure Database is available at https://rna.liacs.nl. The search algorithm is available at https://github.com/LeidenRNA/SRHS. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Authors 5

1. Alan Zammit Aachen Group Imaging and Bioinformatics Leiden Institute of Advanced Computer Science

   Leiden University

   Affiliation as printed

   Group Imaging & Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University , 2300 RA Leiden, The Netherlands

2. Leon Helwerda Aachen Group Imaging and Bioinformatics Leiden Institute of Advanced Computer Science

   Leiden University

   Affiliation as printed

   Group Imaging & Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University , 2300 RA Leiden, The Netherlands

3. René C. L. Olsthoorn Aachen Group Supramolecular & Biomaterials Chemistry

   Leiden University

   Affiliation as printed

   Group Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University , 2300 RA Leiden, The Netherlands

4. Fons J. Verbeek Aachen Group Imaging and Bioinformatics Leiden Institute of Advanced Computer Science

   Leiden University

   Affiliation as printed

   Group Imaging & Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University , 2300 RA Leiden, The Netherlands

5. Alexander P. Gultyaev corresponding Aachen Group Imaging and Bioinformatics Leiden Institute of Advanced Computer Science

   Leiden University · Erasmus MC

   Affiliation as printed

   Department of Viroscience, Erasmus Medical Center , Rotterdam, 3000 CA, The Netherlands

   Group Imaging & Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University , 2300 RA Leiden, The Netherlands