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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

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ProPIP: a tool for progressive multiple sequence alignment with Poisson Indel Process.

Massimo Maiolo^1,2, Lorenzo Gatti^1,2, Diego Frei³

¹Institute of Applied Simulation, School of Life Sciences and Facility Management, Zurich University of Applied Sciences (ZHAW), Schloss 1, Postfach, 8820, Wädenswil, Switzerland.

BMC Bioinformatics

|October 25, 2021

Summary

This summary is machine-generated.

This study introduces ProPIP, a new multiple sequence alignment tool that uses an explicit evolutionary model for insertions and deletions (indels) to prevent over-alignment and infer gaps phylogenetically. ProPIP offers biologically interpretable parameters for improved alignment accuracy.

Keywords:

Alignment software Dynamic programming Evolutionary alignment Indel evolution Multiple sequence alignmnet Poisson Indel Process

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Area of Science:

Bioinformatics
Computational Biology
Evolutionary Biology

Background:

Current multiple sequence alignment tools often lack explicit models for indel evolution.
This deficiency can lead to over-alignment, where inferred alignments are artificially short due to phylogenetic inconsistencies.

Purpose of the Study:

To introduce ProPIP, a novel progressive multiple sequence alignment tool.
To address over-alignment by incorporating an explicit evolutionary model for indel processes.

Main Methods:

ProPIP utilizes the Poisson Indel Process (PIP) to model insertions and deletions.
The method employs dynamic programming within a frequentist framework.
The tool is implemented in C++ and available for Linux, macOS, and Windows.

Main Results:

ProPIP successfully avoids over-alignment by using a phylogenetically consistent approach to gap inference.
The tool enables inferences regarding insertion and deletion rates.
Alignment parameters are based on biologically interpretable insertion and deletion rates rather than arbitrary gap penalties.

Conclusions:

The explicit indel evolution model in ProPIP enhances the phylogenetic consistency of inferred gaps.
Optimizing indel rate settings allows for the inference of phylogenetically meaningful gap patterns.
ProPIP provides a more biologically grounded approach to multiple sequence alignment.