exonize 1.1.1

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. In addition, exonize categorizes the interdependence between duplicated exons (or groups of exons) across transcripts. For data parsing and downstream analysis, the exonize_analysis module is available for Python notebooks.

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]: exonize uses the tblastx program for conducting the local search.
• MUSCLE [download link]: used for conducting the global search and correcting the identity of reconciled matches.
• SQLite[download link]: for storing the search results.

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