MOTIFs

General purpose motif discovery package that includes the discovery of flexible (long or gapped) motifs.

This motif discovery package is currently being actively developed and the method is currently under review with a journal.

Motivation

(coming soon)

Installation

To install MOTIFs.jl use Julia's package manager:

pkg> add MOTIFs

Usage

using MOTIFs

# Do motif discovery on a set of DNA sequences in a fasta file, where the `<fasta-path>` and `<output-folder-path>` are the absolute filepaths as strings.

discover_motifs(<fasta-path>, <output-folder-path>)

# for example

discover_motifs("home/shane/mydata/fasta.fa", "home/shane/mydata/out/")

Interpret the results

(coming soon)

Software requirements

This package currectly requires Weblogo for PWM plotting. Install Weblogo by running the following command with python3 and pip3:

pip3 install weblogo

Hardware requirements

For now, a GPU is required for this package due to the use of CUDA.jl to accelerate some computations. I plan to implement a CPU extension in the near future.

Adjustable Hyperparameters

# The user can adjust the number of epochs for training the network.
discover_motifs(<fasta-path>, <output-folder-path>; num_epochs=10)

Contact

If you have any questions or suggestions regarding the usage or source code, please feel free to reach out to me at skchu@wustl.edu.