This is a Preprint and has not been peer reviewed. The published version of this Preprint is available: https://doi.org/10.1093/gbe/evae011. This is version 1 of this Preprint.
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Abstract
Comparative sequence analysis permits unravelling the molecular processes underlying gene evolution. Many statistical methods generate candidate positions within genes, such as fast or slowly-evolving sites, coevolving groups or residues, sites undergoing positive selection or changes in evolutionary rates. Understanding the functional causes of these evolutionary patterns requires combining the results of these analyses and mapping them onto molecular structures, a complex task involving distinct coordinate referential systems. To ease this task, we introduce the site/group extended data (SGED) format, a simple text format to store (groups of) site annotations. We developed a toolset, the SgedTools, which permits SGED files manipulation, creating them from various software outputs and translating coordinates between individual sequences, alignments, and three-dimensional structures. The package also includes a Monte-Carlo procedure to generate random site samples, possibly conditioning on site-specific features. This eases the statistical testing of evolutionary hypotheses, accounting for the structural properties of the encoded molecules.
DOI
https://doi.org/10.32942/X26K70
Subjects
Life Sciences
Keywords
molecular evolution, Bioinformatics, Data analysis, Three-dimensional struture, randomization
Dates
Published: 2023-11-30 01:39
Last Updated: 2023-11-30 06:39
License
CC BY Attribution 4.0 International
Additional Metadata
Language:
English
Conflict of interest statement:
None.
Data and Code Availability Statement:
Open data and code available at https://github.com/jydu/sgedtools/
There are no comments or no comments have been made public for this article.