:: DESCRIPTION
RILogo is a software for displaying sequence logos and base pairing between two RNA sequences/alignments.
::DEVELOPER
Center for non-coding RNA in Technology and Health (RTH)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
P. Menzel, S.E. Seemann, J. Gorodkin.
RILogo: Visualising RNA-RNA interactions,
Bioinformatics (2012) 28 (19): 2523-2526. doi: 10.1093/bioinformatics/bts461
:: DESCRIPTION
RIsearch is a program for fast RNA-RNA interaction search. It employs a modified Smith-Waterman-Gotoh algorithm based on di-nucleotides to approximate nearest-neighbor energy parameters.
::DEVELOPER
Center for non-coding RNA in Technology and Health (RTH)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Alkan F, Wenzel A, Palasca O, Kerpedjiev P, Rudebeck AF, Stadler PF, Hofacker IL, Gorodkin J.
RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets.
Nucleic Acids Res. 2017 May 5;45(8):e60. doi: 10.1093/nar/gkw1325. PMID: 28108657; PMCID: PMC5416843.
Bioinformatics. 2012 Aug 24. [Epub ahead of print]
RIsearch: Fast RNA-RNA interaction search using a simplified nearest-neighbor energy model.
Wenzel A, Akbasli E, Gorodkin J.
:: DESCRIPTION
SilentMutations (SIM) can analyze the effect of multiple point mutations on the secondary structures of two interacting viral RNAs. It simulates destructive and compensatory mutants of two key regions from a single-stranded RNA, which can then be utilized for the combinatorial in vitro analysis of RNA-RNA interactions.
::DEVELOPER
RNA Bioinformatics and High Throughput Analysis Jena
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
D. Desiro, M. Hölzer, B. Ibrahim, and M. Marz,
SilentMutations (SIM): a tool for analyzing long-range RNA-RNA interactions in viral genomes and structured RNAs
Virus Res. 2019 Jan 15;260:135-141. doi: 10.1016/j.virusres.2018.11.005. Epub 2018 Nov 12.
