Tools & Software

ScanFold - a computational tool for scanning for long RNA sequences for evidence of local ordered structural motifs with possible function. Available in three formats:

• Source Code - ScanFold source code available on GitHub

• Web server - ScanFold calculations can be run via an ISU hosted web server

• IGV-ScanFold - ScanFold has been implemented within the integrative genomics viewer (IGV)
  
  

Citation:
Andrews RJ, Roche J, Moss WN. ScanFold: an approach for genome-wide discovery of local RNA structural elements-applications to Zika virus and HIV. PeerJ. 2018;6:e6136.

RNA2DMut- a tool for generating and evaluating the impact of all possible mutations on RNA secondary structure: e.g. point mutations, indels, randomization, etc. As well as evaluating multiple sequences. Program implements the popular RNAfold algorithm.
Available in two formats:

Web server - RNA2DMut calculations can be run via an ISU hosted web server

Source Code - RNA2DMut source code is available on GitHub

Citation:
Moss WN. RNA2DMut: a web tool for the design and analysis of RNA structure mutations. RNA. 2018 Mar;24(3):273-286.

RNAStructuromeDB - The RNA structurome database is an online repository of RNA structural information spanning human and pathogen genomes. Data include ScanFold genome and transcriptome scans and model structures of highly significant motifs.

Citation:
Andrews RJ, Baber L, Moss WN. RNAStructuromeDB: A genome-wide database for RNA structural inference. Sci Rep. 2017 Dec 8;7(1):17269.