PAN_Alleleome: Alleleome Generation for Pan-Genomes of Species

Introduction

"PAN_Alleleome" is a specialized package designed to explore and analyze natural sequence variations within the Open Reading Frames (ORFs) of alleles of all genes in a species' pan-genome, both at the amino acid and nucleotide levels. This first version focuses on analyzing the genes of a pan-genome. It identifies variants such as substitutions, insertions, and deletions through a series of steps:

1. Initial QCQA of sequences.
2. Building consensus for each gene's allele set.
3. Pairwise alignment of consensus sequences with individual alleles.
4. Identification and generation of amino acid variant datasets.
5. Analysis of synonymous and non-synonymous substitutions from codons and corresponding amino acid data.

The PAN_Alleleome workflow is tailored to study the natural sequence variations in the genes of the pan-genome of a species, with an emphasis on variations at the amino acid and nucleotide level.

Table of Contents

• Introduction
• Getting Started
• Usage
• Features
• Built With
• Versioning
• Authors and Acknowledgment
• License

Getting Started

Prerequisites

• PAN_Alleleome is tested and confirmed for Linux systems with the Conda package manager.
• Requires Python version 3.10 or higher.
• For optimal performance, especially when processing a large dataset, such as 3400 genes and their respective alleles across 3400 strains, a high RAM capacity is strongly recommended.

Installation

Using GitHub Repository

1. Clone the repository:

   git clone https://github.com/anpanche/PAN_Alleleome.git
   

2. Navigate to the Alleleome directory:

   cd PAN_Alleleome
   

3. Install the package:

   pip install .
   

Usage

Test Sample Data Run

Run Alleleome with sample data using:

PAN_Alleleome

Refer to the sample_data directory for output organization and details.

Running Your Species Pangenes

To analyze your species data:

PAN_Alleleome --path1 path/to/pangenome_alignments --path2 path/to/alleleome

Features

PAN_Alleleome introduces the concept of "ORF alleleome," encapsulating the gene alleles found across all strains of a species, thus providing a comprehensive view of genome-scale sequence variations. This analysis can be instrumental in understanding sequence diversity characteristics and natural selection processes across different species within a family. The study of the alleleome offers insights into the genetic basis of natural selection in a species.

Key features include:

• Analysis of sequence variants using the consensus sequence of ORFs.
• Identification of dominant amino acids and their variants at specific positions.
• Revealing natural sequence and structural variations compared with the consensus sequence and structural attributes.
• Identification of genome-scale synonymous and non-synonymous mutations through the analysis of codon changes and their corresponding amino acid changes."

Built With

• Python and Biopython.
• Integrated with "BGCflow" workflow using SnakeMake.

License

This project is licensed under the MIT License - see the LICENSE file for details.