TY - JOUR
AU - Szachniuk, Marta
AB - Background: The function of RNA is strongly dependent on its structure, so an appropriate recognition of this structure, on every level of organization, is of great importance. One particular concern is the assessment of base- base interactions, described as the secondary structure, the knowledge of which greatly facilitates an interpretation of RNA function and allows for structure analysis on the tertiary level. The RNA secondary structure can be predicted from a sequence using in silico methods often adjusted with experimental data, or assessed from 3D structure atom coordinates. Computational approaches typically consider only canonical, Watson-Crick and wobble base pairs. Handling of non-canonical interactions, important for a full description of RNA structure, is still very difficult. Results: We introduce our novel approach to assessing an extended RNA secondary structure, which characterizes both canonical and non-canonical base pairs, along with their type classification. It is based on predicting the RNA 3D structure from a user-provided sequence or a secondary structure that only describes canonical base pairs, and then deriving the extended secondary structure from atom coordinates. In our example implementation, this was achieved by integrating the functionality of two fully automated, high fidelity methods in a computational pipeline: RNAComposer for the 
TI - New in silico approach to assessing RNA secondary structures with non-canonical base pairs
JO - BMC Bioinformatics
DO - 10.1186/s12859-015-0718-6
DA - 2015-09-02
UR - https://www.deepdyve.com/lp/springer-journals/new-in-silico-approach-to-assessing-rna-secondary-structures-with-non-knl2phPOJV
SP - 1
EP - 12
VL - 16
IS - 1
DP - DeepDyve
ER -