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IntaRNA (version 3.4.0)
Query Parameters
Query Parameters 0
Target Parameters
Target Parameters 0
Seed Parameters
Seed Parameters 0
Interaction Parameters
Interaction Parameters 0
Output Options
Output Options 0

What it does Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites During the last few years, several new small regulatory RNAs (sRNAs) have been discovered in bacteria. Most of them act as post-transcriptional regulators by base pairing to a target mRNA, causing translational repression or activation, or mRNA degradation. Numerous sRNAs have already been identified, but the number of experimentally verified targets is considerably lower. Consequently, computational target prediction is in great demand. Many existing target prediction programs neglect the accessibility of target sites and the existence of a seed, while other approaches are either specialized to certain types of RNAs or too slow for genome-wide searches. IntaRNA, developed by Prof. Backofen's bioinformatics group at Freiburg University, is a general and fast approach to the prediction of RNA-RNA interactions incorporating both the accessibility of interacting sites as well as the existence of a user-definable seed interaction. We successfully applied IntaRNA to the prediction of bacterial sRNA targets and determined the exact locations of the interactions with a higher accuracy than competing programs. .. class:: infomark Please refer to IntaRNA github repository for use cases and additional information. Input RNA sequences in FASTA format Output RNA-RNA interaction information in CSV format and additional information/files on demand