New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation.

ABSTRACT:

Motivation

Understanding the formation, architecture and roles of pseudoknots in RNA structures are one of the most difficult challenges in RNA computational biology and structural bioinformatics. Methods predicting pseudoknots typically perform this with poor accuracy, often despite experimental data incorporation. Existing bioinformatic approaches differ in terms of pseudoknots' recognition and revealing their nature. A few ways of pseudoknot classification exist, most common ones refer to a genus or order. Following the latter one, we propose new algorithms that identify pseudoknots in RNA structure provided in BPSEQ format, determine their order and encode in dot-bracket-letter notation. The proposed encoding aims to illustrate the hierarchy of RNA folding.

Results

New a

SUBMITTER: Antczak M 

PROVIDER: S-EPMC5905660 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature