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moss-lab / ScanFold

ScanFold is an RNA sequence scanning pipeline which attempts to identify potentially functional RNA secondary structures. This is done by first scanning a single input sequence to identify regions which generate negative thermodynamic z-scores (a hallmark of functional RNA sequences), and subsequently identifying the specific base pairs which were responsible for generating the low z-scores.
https://peerj.com/articles/6136/
MIT License
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ScanFold

ScanFold has been implemented as a WebServer. Try it out at https://mosslabtools.bb.iastate.edu/scanfold1 and read more about its uses here: https://doi.org/10.1016/j.ymeth.2019.11.001

The ScanFold pipeline is a set of scripts which scan a large RNA sequence (using ScanFold-Scan.py) and subsequently extract structural motifs (using ScanFold-Fold.py) which have evidence of being ordered by evolution to form an unusually stable structure (potentially to serve a functional role).

Updates

(Update from 2/17/2021) ScanFold-Scan and ScanFold-Fold have been combined into a single script called ScanFold.py. This script can incorporate soft constraints as pseudo energies using RNAfold's implementation of the Deigan or Zarringhalam algorithms.

(Update from 12/10/2019) ScanFold-Scan can now consider hard constraints as input during the scanning window process. Constraints should be formatted as .dbn files, where line 1 is a header, line 2 is the sequence and line three contains the hard constraints.

Here's a list of allowed constraints (https://www.tbi.univie.ac.at/RNA/RNAfold.1.html#heading6):

Dependencies

The ScanFold-Scan.py and ScanFold-Fold.py scripts were built using Python3.6 and utilize several outside python modules.

ScanFold-Scan dependencies:

  1. ViennaRNA; Must ensure that python3.6 can import "RNA" as a module. See details for that here: https://www.tbi.univie.ac.at/RNA/documentation.html#install
  2. NumPy (www.numpy.org/)
  3. SeqIO from BioPython (https://biopython.org/wiki/SeqIO)

ScanFold-Fold dependencies:

  1. RNAStructure (https://rna.urmc.rochester.edu/Overview/Python.html)

ScanFold.py dependencies:

  1. ViennaRNA
  2. SeqIO from BioPython