RNA Secondary Structure Database, Analysis Tool-Set, and Case-Study Results on SARS-CoV-2

ABSTRACT

COVID-19 pandemic has brought immense attention to SARS-CoV-2 and related microbiology studies. To defeat this deadly virus, its RNA is being studied by many researchers around the globe. This study primarily aims to compile a large RNA dataset to analyze RNA secondary structure of SARS-CoV-2 efficiently. We propose improvements on database creation and maintenance, and structure analysis tools. As a continuation of our previous works, we automate the creation of RNA secondary structures database in a new format by converting data collected from publicly available online resources. We present new secondary structure analysis algorithms that improve performance of existing tools. Results of GPU-based implementation are also presented for RNA search operations. We also introduce tools with new objectives, which answer fundamental RNA secondary structure queries. Our tools on the current database have been tested with SARS-CoV-2 related RNA secondary structures. A novel RNA secondary structure search-based multiple RNA comparison is introduced and tested too. Structural-only and structure-with-nucleotide search results particularly related to SARS-CoV-2 are presented in details. As a successful case study, the framework presented here offers some unique capabilities and is shown as a useful exploratory tool for future RNA analysis studies. © 2021 IEEE.