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MutaNET

Introduction

Mutations in genomic key elements can influence gene expression and function in various ways, and hence greatly contribute to the phenotype. MutaNET comes with a next generation sequencing (NGS) pipeline that calls mutations based on paired-end NGS reads, an automated analysis tool and various file converters and mergers. The mutation analysis feature considers the coding region, protein domains, regulation and transcription factor binding site information, and can be used to analyse the potential impact of mutations on genes of interest.

MutaNET was developed and implemented in 2017 and published in 2018:

Hollander, M, Hamed, M, Helms, V, Neininger, K (2018). MutaNET: a tool for automated analysis of genomic mutations in gene regulatory networks. Bioinformatics, 34, 5:864-866. https://www.ncbi.nlm.nih.gov/pubmed/29087464

Descriptions, explanations and examples of functionality and data sources can be found in user_manual.pdf. Detailed installation instructions for Windows, Linux and Mac OS X can be found in installation_guide.pdf.

Quickstart

Starting MutaNET

MutaNET comes as Python 3 source code. Open a command prompt or terminal and execute the following command:

python3 source_folder_path/mutaNET.py

or on Windows depending on your Python installation:

python source_folder_path/mutaNET.py

Source_folder_path is the path to the folder containing the source code of MutaNET. This requires Python 3 to be installed.

Example Data Sets

When starting MutaNET for the first time, the file paths for small example data sets for the NGSpipeline, mutation analysis and file converters are already loaded to allow quick testing. Keep in mind that for the NGS pipeline extra programs need to be installed. The settings for the example data can be restored any time by clicking on Settings → Restore default settings. The data sets can be found in the example_data folder, if you want to have a look at the file formats.

NGS Pipeline: You need to extract S11_R1.fastq and S11_R2.fastq from S11_R1.zip and S11_R2.zip in example_data/NGS/reads before running the NGS pipeline with the example data.

Change Log

Version 1.1.2

  • updated the file converter to account for changes made to RegulonDB
  • removed the pre-compiled executables for Windows due to incompatible changes made to PyInstaller

Version 1.1.1

  • updated installation instructions and installation script of SAMTools, VarScan and BWA for MacOS
  • updated the UniProt converter to handle the new UniProt format

Version 1.1.0

  • added support for eukaryotes
  • fixed file encoding issues
  • fixed minor frame shift bug