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

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

SUBMITTER: Zammit A 

PROVIDER: S-EPMC8128465 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature