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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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paPAML: An Improved Computational Tool to Explore Selection Pressure on Protein-Coding Sequences.

Raphael Steffen¹, Lynn Ogoniak^1,2, Norbert Grundmann²

¹Institute of Experimental Pathology, ZMBE, University of Münster, 48149 Münster, Germany.

|June 24, 2022

Summary

This summary is machine-generated.

We developed paPAML, a tool that accelerates evolutionary selection analyses on protein-coding DNA sequences (CDS). This method simplifies complex analyses and speeds up computation, aiding in the detection of negative selection.

Keywords:

CDS-extractor HyPhy PAML abalone sperm lysin apolipoprotein codeml neutrophil associated gene paPAML positive selection purifying selection retrotransposon exonization

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Area of Science:

Evolutionary Biology
Molecular Evolution
Bioinformatics

Background:

Phylogenetic reconstructions rely on neutral evolutionary changes.
Selection-relevant changes in protein-coding DNA sequences (CDS) offer insights into evolutionary pressures.
Analyzing the ratio of nonsynonymous to synonymous mutations measures selection pressure.

Purpose of the Study:

To develop a tool that simplifies and accelerates evolutionary selection analyses of CDS.
To enhance the detection of negatively selected sites.
To provide a user-friendly alternative for analyzing evolutionary constraints.

Main Methods:

Developed CDS extractor for compiling protein-coding sequences.
Created parallel PAML (paPAML) for accelerated selection analyses via parallel processing.
Applied paPAML to analyze evolutionary impact on specific genes (GINS Complex Subunit 3, neutrophil-associated, lysin, apolipoprotein).

Main Results:

paPAML provides identical selection pressure results to existing tools (codeml, HyPhy FEL).
paPAML significantly accelerates total selection analysis, being 3-5 times faster than codeml and 7-15 times faster than full codeml processing.
The tool successfully detects site-specific negative selection and simplifies analysis for users.

Conclusions:

paPAML is an efficient and user-friendly tool for evolutionary selection analyses.
The developed tool accelerates computational speed without compromising accuracy.
paPAML facilitates deeper understanding of episodic constraints, relaxed selection, and adaptive evolution in protein-coding genes.