Pairwise visual comparison of small RNA secondary structures with base pair probabilities
Abstract Background Predicted RNA secondary structures are typically visualized using dot-plots for base pair binding probabilities and planar graphs for unique structures, such as the minimum free energy structure. These are however difficult to analyze simultaneously. Results This work introduces...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2019-05-01
|
| Series: | BMC Bioinformatics |
| Online Access: | http://link.springer.com/article/10.1186/s12859-019-2902-6 |
| _version_ | 1811323285060714496 |
|---|---|
| author | Serge Léger Maria Beatriz Walter Costa Dan Tulpan |
| author_facet | Serge Léger Maria Beatriz Walter Costa Dan Tulpan |
| author_sort | Serge Léger |
| collection | DOAJ |
| description | Abstract Background Predicted RNA secondary structures are typically visualized using dot-plots for base pair binding probabilities and planar graphs for unique structures, such as the minimum free energy structure. These are however difficult to analyze simultaneously. Results This work introduces a compact unified view of the most stable conformation of an RNA secondary structure and its base pair probabilities, which is called the Circular Secondary Structure Base Pairs Probabilities Plot (CS 2 BP 2 -Plot). Along with our design we provide access to a web server implementation of our solution that facilitates pairwise comparison of short RNA (and DNA) sequences up to 200 base pairs. The web server first calculates the minimum free energy secondary structure and the base pair probabilities for up to 10 RNA or DNA sequences using RNAfold and then provides a two panel comparative view that includes CS2BP2-Plots along with the traditional graph, planar and circular diagrams obtained with VARNA. The CS2BP2-Plots include highlighting of the nucleotide differences between two selected sequences using ClustalW local alignments. We also provide descriptive statistics, dot-bracket secondary structure representations and ClustalW local alignments for compared sequences. Conclusions Using circular diagrams and colour and weight-coded arcs, we demonstrate how a single image can replace the state-of-the-art dual representations (dot-plots and minimum free energy structures) for base-pair probabilities of RNA secondary structures while allowing efficient exploration and comparison of different RNA conformations via a web server front end. With that, we provide the community, especially the biologically oriented, with an intuitive tool for ncRNA visualization. Web-server: https://nrcmonsrv01.nrc.ca/cs2bp2plot |
| first_indexed | 2024-04-13T13:51:19Z |
| format | Article |
| id | doaj.art-9b4a9f17747544ceb2675f6cda7fa4d3 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-13T13:51:19Z |
| publishDate | 2019-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-9b4a9f17747544ceb2675f6cda7fa4d32022-12-22T02:44:19ZengBMCBMC Bioinformatics1471-21052019-05-0120111210.1186/s12859-019-2902-6Pairwise visual comparison of small RNA secondary structures with base pair probabilitiesSerge Léger0Maria Beatriz Walter Costa1Dan Tulpan2Digital Technologies Research Center, National Research Council CanadaDepartment of Computer Science, TFome Research Group, Bioinformatics Group, Interdisciplinary Center of Bioinformatics, University of LeipzigDepartment of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of GuelphAbstract Background Predicted RNA secondary structures are typically visualized using dot-plots for base pair binding probabilities and planar graphs for unique structures, such as the minimum free energy structure. These are however difficult to analyze simultaneously. Results This work introduces a compact unified view of the most stable conformation of an RNA secondary structure and its base pair probabilities, which is called the Circular Secondary Structure Base Pairs Probabilities Plot (CS 2 BP 2 -Plot). Along with our design we provide access to a web server implementation of our solution that facilitates pairwise comparison of short RNA (and DNA) sequences up to 200 base pairs. The web server first calculates the minimum free energy secondary structure and the base pair probabilities for up to 10 RNA or DNA sequences using RNAfold and then provides a two panel comparative view that includes CS2BP2-Plots along with the traditional graph, planar and circular diagrams obtained with VARNA. The CS2BP2-Plots include highlighting of the nucleotide differences between two selected sequences using ClustalW local alignments. We also provide descriptive statistics, dot-bracket secondary structure representations and ClustalW local alignments for compared sequences. Conclusions Using circular diagrams and colour and weight-coded arcs, we demonstrate how a single image can replace the state-of-the-art dual representations (dot-plots and minimum free energy structures) for base-pair probabilities of RNA secondary structures while allowing efficient exploration and comparison of different RNA conformations via a web server front end. With that, we provide the community, especially the biologically oriented, with an intuitive tool for ncRNA visualization. Web-server: https://nrcmonsrv01.nrc.ca/cs2bp2plothttp://link.springer.com/article/10.1186/s12859-019-2902-6 |
| spellingShingle | Serge Léger Maria Beatriz Walter Costa Dan Tulpan Pairwise visual comparison of small RNA secondary structures with base pair probabilities BMC Bioinformatics |
| title | Pairwise visual comparison of small RNA secondary structures with base pair probabilities |
| title_full | Pairwise visual comparison of small RNA secondary structures with base pair probabilities |
| title_fullStr | Pairwise visual comparison of small RNA secondary structures with base pair probabilities |
| title_full_unstemmed | Pairwise visual comparison of small RNA secondary structures with base pair probabilities |
| title_short | Pairwise visual comparison of small RNA secondary structures with base pair probabilities |
| title_sort | pairwise visual comparison of small rna secondary structures with base pair probabilities |
| url | http://link.springer.com/article/10.1186/s12859-019-2902-6 |
| work_keys_str_mv | AT sergeleger pairwisevisualcomparisonofsmallrnasecondarystructureswithbasepairprobabilities AT mariabeatrizwaltercosta pairwisevisualcomparisonofsmallrnasecondarystructureswithbasepairprobabilities AT dantulpan pairwisevisualcomparisonofsmallrnasecondarystructureswithbasepairprobabilities |