@article{Miladi-2020-MutaRNA,
author = {Miladi, Milad and Raden, Martin and Diederichs, Sven and Backofen, Rolf},
title = {{MutaRNA}: analysis and visualization of mutation-induced changes in {RNA} structure},
journal = {Nucleic Acids Research},
year = {2020},
doi = {10.1093/nar/gkaa331},
volume = {},
user = {mmann},
pages = {},
number = {},
note = {(MM and MR contributed equally)},
month = {05},
issn = {0305-1048},
eprint = {https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkaa331/33202973/gkaa331.pdf},
abstract = {RNA molecules fold into complex structures as a result of intramolecular interactions between their nucleotides. The function of many non-coding RNAs and some cis-regulatory elements of messenger RNAs highly depends on their fold. Single-nucleotide variants (SNVs) and other types of mutations can disrupt the native function of an RNA element by altering its base pairing pattern. Identifying the effect of a mutation on an RNA’s structure is, therefore, a crucial step in evaluating the impact of mutations on the post-transcriptional regulation and function of RNAs within the cell. Even though a single nucleotide variation can have striking impacts on the structure formation, interpreting and comparing the impact usually needs expertise and meticulous efforts. Here, we present MutaRNA, a web server for visualization and interpretation of mutation-induced changes on the RNA structure in an intuitive and integrative fashion. To this end, probabilities of base pairing and position-wise unpaired probabilities of wildtype and mutated RNA sequences are computed and compared. Differential heatmap-like dot plot representations in combination with circular plots and arc diagrams help to identify local structure abberations, which are otherwise hidden in standard outputs. Eventually, MutaRNA provides a comprehensive and comparative overview of the mutation-induced changes in base pairing potentials and accessibility. The MutaRNA web server is freely available at http://rna.informatik.uni-freiburg.de/MutaRNA.}
}