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


[ 1 ] Instytut Informatyki, Wydział Informatyki, Politechnika Poznańska | [ 2 ] Instytut Chemii Bioorganicznej PAN | [ P ] employee

Scientific discipline (Law 2.0)

[2.3] Information and communication technology
[7.6] Chemical sciences

Year of publication


Published in


Journal year: 2018 | Journal volume: vol. 34 | Journal number: iss. 8

Article type

scientific article

Publication language



EN 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 algorithms are based on dynamic programming and hybrid (combining exhaustive search and random walk) approaches. They evolved from elementary algorithm implemented within the workflow of RNA FRABASE 1.0, our database of RNA structure fragments. They use different scoring functions to rank dissimilar dot-bracket representations of RNA structure. Computational experiments show an advantage of new methods over the others, especially for large RNA structures.

Pages (from - to)

1304 - 1312




License type

CC BY-NC (attribution - noncommercial)

Open Access Mode

open journal

Open Access Text Version

final published version

Date of Open Access to the publication

at the time of publication

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