exonize 1.1.2

A tool for finding duplicated exons in annotated genomes

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Marina Herrera Sarrias, Department of Mathematics, Stockholm University
Christopher Wheat, Department of Zoology, Stockholm University
Liam M. Longo, Earth-Life Science Institute (ELSI), Institute of Science Tokyo
Lars Arvestad, Department of Mathematics, Stockholm University

Welcome!

exonize is an open-source command-line tool and Python package for identifying and classifying coding exon duplications in annotated genomes. exonize identifies full exon duplications using local and global alignment methods and implements a graph-based framework to handle clusters of exons formed by repetitive duplication events. exonize introduces a classification schema to categorize the interdependence between duplicated exons (or groups of exons) across transcripts. For data parsing and downstream analysis, we introduce exonize_analysis a Python module within the exonize package.

Documentation

Please see the Documentation for a full user guide and an introductory tutorial to the exonize_analysis module.

Installation

You are best off installing exonize from PyPI.org using

pip install exonize

If installing from the GitHub repo

git clone [e-mail]:msarrias/exonize.git
cd exonize
pip install .

You should now be able to run exonize -h.

exonize is tested with Python 3.9, 3.10, 3.11, 3.12

Requirements

exonize requires a local installation of:

• BLAST+ [download link]
• MUSCLE (v.5.3) [download link]
• SQLite[download link]

Support

If you need help with exonize, contact us! To report a bug or request a new feature, open an Issue on the exonize repo.

Citation

If you use exonize in a publication, please cite:

TBA