multiMotif 1.2.5

A Computational Tool for Variable Motif scanning and Sequence-based Relative Position Visualization of Search Results in Sequences.

multiMotif

A tool for Scanning and Visualization of Diverse and Distant Multiple Motifs.

Installation

To install multiMotif, you can use pip:

pip install multiMotif

Or clone the repository and then install it local:

git clone https://github.com/SainanLuo/multiMotif.git
cd multiMotif
pip install .

If you are a Windows user, make sure you installed Python3, then run this command in your cmd or PowerShell:

C:\Users\lsn> set PATH=C:\Users\lsn\AppData\Local\Programs\Python\Python311 #set your Python path in cmd window
C:\Users\lsn> set PATH=C:\Users\lsn\AppData\Local\Programs\Python\Python311\Scripts #set your pip path in cmd window
C:\Users\lsn> pip install multiMotif
C:\Users\lsn> multiMotif -h

Dependencies

multiMotif requires the following packages:

Biopython (>= 1.78)

Matplotlib (>= 3.3)

NumPy (>= 1.19)

Pandas (>= 1.1)

plotly (>=5.18.0)

These dependencies will be installed automatically when you install multiMotif using pip.

Usage

After installation, you can use the multiMotif command to run multiMotif. Here is the basic usage:

usage: multiMotif [-h]
                  {singleMotif,multiMotif,visualMotif,extract_sequences} ...

VariaMotif for motif scanning

positional arguments:
  {singleMotif,multiMotif,visualMotif,extract_sequences}
                        sub-command help
    singleMotif         Scanning for single motif
    multiMotif          Scanning more than two ordered motifs
    visualMotif         Visualization:display motif in sequence
    extract_sequences   Extract Sequences

optional arguments:
  -h, --help            show this help message and exit

multiMotif tool features modules for identifying single motifs(‘singleMotif’), multiple motifs(‘multiMotif’), a visualization module (‘visualMotif’) to enhance results interpretation, and a sequence extraction module (‘extract_sequences’) for obtaining promoters or open reading frames, or user-specified locations.

We provide comprehensive user manuals in both Chinese and English. You can download the English version of the manual at English Language User Manual Download Link. For the Chinese version, please visit this link:Chinese Language User Manual Download Link.