Installation

The recommended way to setup your computer for running Inimotif is to install the official distribution of Python 3.7. You can download the official Python 3.7 distribution here.

Once you've installed Python, download the zip file of IniMotif from this repository (click Clone or download on top right corner). Decompress this zip file and open the terminal/prompt and change to this directory.

In Linux and Mac, enter the following command:

pip install -r requirements.txt

In Windows, enter the following command:

py -m pip install -r requirements.txt

This will install the required python packages that Inimotif needs to run. Note that Inimotif may work for versions of Python 3 prior to 3.7, but this is untested. For Mac you may need to update Tcl/Tk to use the GUI for versions of Python prior to 3.7.2. See here for more information.

Alternatively, you can also run Inimotif using Anaconda. To setup a conda environment and install the requirements:

conda create -y --name inimotif python==3.7
conda install -fyq --name inimotif -c conda-forge --file requirements.txt
conda activate inimotif

Run IniMotif

Open the GUI by opening the directory containing the python files in a terminal, and run the inimotif_gui.py using python.

In Linux and Mac, enter the following command to run inimotif

$ python inimotif_gui.py

In Windows, enter the following command to run inimotif

$ py inimotif_gui.py

This will start the GUI of IniMotif. Select from one of the three options: ChP-seq, SELEX-seq, or Masker. Check the following tutorials for detailed function explanations.

Tutorials

We will go through all functionalities of IniMtoif in the following list of tutorials.

• Terms explanation
  • kmer
  • Reverse complement
  • Palindrome
  • Motif
  • Motif logo
• ChIP-seq Analysis
  • Motif discovery from ChIP-seq data
  • Query kmers
  • Scan motifs
• SELEX-seq Analysis
  • Motif discovery of SELEX-seq data
  • Query kmers
  • Scan motifs
• Sequence masking
  • Mask repetitive patterns
  • Mask motifs
• Downloading datasets from European Nucleotide Archive
  • Downloading all relevant datasets by "accession number" using scripts
• Extracting ChIP-seq windows from reference genome
  • Extract sequences from given ChIP-seq windows on reference genome