lemora / msa-proteoform-profiler

Detect and annotate proteoforms/domains from RNA-Seq multiple sequence alignments

The MSA Proteoform Profiler

Overview

The MSAPP is a tool for high-level analysis of RNA-Seq multiple sequence alignments. It assists in detecting and annotating proteoforms and domains.

It can either be run with a graphical user interface (recommended), or as a command-line tool.

Dependencies

This software requires python >= 3.9 and poetry. All package versions are managed by poetry.

Running

Create a virtual environment with an appropriate python version (once): poetry env use python3.12.

Activate the virtual environment: poetry shell. Then prepare by installing: poetry install.

The Graphical User Interface

The GUI mode is currently the recommended way to use the MSAPP. It allows interactive analysis and fine-tuning of filtering parameters and similarity cutoff levels.

Running the GUI:

msapp-gui

Or, when not in venv: poetry run msapp-gui.

The Command-Line Interface

The CLI offers similar tuning/visualization parameters as the GUI, but it is less interactive.

Running the CLI:

msapp [options] <msa file>

Or, when not in venv: poetry run msapp [options] <msa file>.

License

This software is licensed under GPLv3.0 or later.