About

RNAfoldml is an OCaml package that enables users to input both RNA sequences in FASTA format and a set of constraints to predict RNA secondary structure.

Key Features

• Parsing of RNA sequences inputted in text-based FASTA format
• Implementation of folding algorithms developed by Nussinov and Zuker for free energy minimization
• Usable OCaml package with functions which generate formatted secondary structure output from
• Online documentation for package
• Formatted output includes:
  • Description of parameters, algorithm, time, input sequence
  • Table describing RNA sequence pairing
  • Graphical representation of RNA secondary structures

Authors

• Inle Bush
• Jan-Paul Ramos
• Songyu Ye

Getting started

1. OCaml 4.0.0+ has to be installed to ensure nothing breaks. This library uses no external dependencies except OUnit2 for tests.

2. Unzip rnafoldml.zip into your preferred directory.

3. Go in the unzipped rnafoldml folder and in the root directory, run make build in your command line. Build the docs with make doc.

4. Use the code in utop with make utop.