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Genome-wide RNA structure prediction on your own laptop using ParasoR

ParasoR can perform RNA secondary structure prediction and a variety of RNA structure analysis by simple command line like below.

    ParasoR --pre -f UCCCG
    ParasoR --pre --input example.fasta

• Tutorial is available here.
• About parallel computation for long sequences, please refer ParasoR model.
• For more detail, check Secondary structure prediction and Basic parameter setting.

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Change log:

• 2023.02.14 -- Update external links and wiki
• 2020.12.28 -- Add a tutorial for simulation with a single point mutation.
• 2018.03.05 -- Fix a harmless bug in BLstar parameter reading process. Recommend to use the latest source codes.
• 2017.07.05 -- Implement MFE structure prediction and interaction energy computation in the latest version (as a prototype version).
• 2016.06.21 -- Some error was reported when calculating structures using short sequences (shorter than the length of maximal span) in ParasoR mode v1.0.0 due to the file name inconsistency.[Fix]
• 2016.05.06 -- v1.0 Released.

External link

• ParasoR (Genome-wide structure analysis)
  • https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1067-9
  • Genome-Wide RNA Secondary Structure Prediction
  • My doctoral thesis for the full detail of ParasoR algorithm
• Radiam (Mutational structure analysis)
  • RNA Secondary Structure Alteration Caused by Single Nucleotide Variants
  • My master's thesis for the full detail of Radiam algorithm
• Others
  • https://omictools.com/parasor-tool