MPGAfold in dengue secondary structure prediction.

ABSTRACT: This chapter presents the computational prediction of the secondary structures within the 5' and 3' untranslated regions of the dengue virus serotype 2 (DENV2), with the focus on the conformational prediction of the two dumbbell-like structures, 5' DB and 3' DB, found in the core region of the 3' untranslated region of DENV2. For secondary structure prediction purposes we used a 719 nt-long subgenomic RNA construct from DENV2, which we refer to as the minigenome. The construct combines the 5'-most 226 nt from the 5' UTR and a fragment of the capsid coding region with the last 42 nt from the non-structural protein NS5 coding region and the 451 nt of the 3' UTR. This minigenome has been shown to contain the elements needed for translation, as well as negative strand RNA synthesis. We present

SUBMITTER: Kasprzak WK 

PROVIDER: S-EPMC6354254 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature