Phage Activation Project

Overview

This project involves genomic analysis for phage activation. It includes scripts to analyze genome sequences using tools like MEME, Needle, and BLASTP.

Installation

Create a Python Environment

To create a new Python environment named Phage_design and install the necessary packages, follow these steps:

# Create a new conda environment
conda create -n Phage_design -y python=3.9

# Activate the environment
conda activate Phage_design

Install Python Dependencies

To install the necessary Python dependencies, run:

pip install -r requirements.txt

Install External Tools

This project requires the following external tools:

1. MEME Suite: For motif-based sequence analysis.
2. Needle: For sequence alignment.
3. BLASTP: For protein-protein sequence alignment.

Installing MEME Suite

To install MEME Suite, follow these steps:

# Download and extract MEME Suite
wget http://meme-suite.org/meme-software/5.4.1/meme-5.4.1.tar.gz
tar -zxvf meme-5.4.1.tar.gz
cd meme-5.4.1

# Configure and install
./configure --prefix=/usr/local
make
sudo make install

Installing Needle

To install Needle, follow these steps:

# On Debian/Ubuntu
sudo apt-get update
sudo apt-get install emboss

# On CentOS/RHEL
sudo yum install epel-release
sudo yum install emboss

After downloading Needle, move it to /usr/bin/:

sudo mv needle /usr/bin/

Installing BLASTP

To install BLASTP, follow these steps:

# Download BLAST+
wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.11.0/ncbi-blast-2.11.0+-x64-linux.tar.gz
tar -zxvf ncbi-blast-2.11.0+-x64-linux.tar.gz
cd ncbi-blast-2.11.0+

# Add BLAST+ to PATH
export PATH=$PATH:$PWD/bin

Installing Prokka

Prokka is a software tool for the rapid annotation of prokaryotic genomes.

To install Prokka, follow these steps:

1. Using Conda (recommended)

   If you have Conda installed, you can easily install Prokka using the Bioconda channel:

   conda install -c conda-forge -c bioconda prokka

Installing CD-HIT

# Download CD-HIT
wget https://github.com/weizhongli/cdhit/releases/download/V4.8.1/cd-hit-v4.8.1-2019-0228.tar.gz
tar -zxvf cd-hit-v4.8.1-2019-0228.tar.gz
cd cd-hit-v4.8.1-2019-0228

# Compile and install
make
sudo cp cd-hit /usr/local/bin
sudo cp cd-hit-est /usr/local/bin

Usage

To run the phage activation analysis, use the following command:

python phage_design.py -fasta_path <path_to_fasta_file> -output_dir <output_directory>

Example

python phage_design.py -gbk_path test_data/KX897981.fasta -output_dir test_data/

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Part 2: Ongoing Work

megaDNA: A Long-Context Language Model for Deciphering and Generating Bacteriophage Genomes

MegaDNA is a long-context language model designed for decoding and generating bacteriophage genomes, pioneered by Shaobin. Inspired by the success of GPT models in natural language processing, MegaDNA has been optimized specifically for genomic data. Using a multiscale Transformer architecture, it is pre-trained on unannotated bacteriophage genomes and can identify essential genes, gene variant effects, regulatory element activity, and classify unannotated sequences.

Currently, we are expanding MegaDNA’s capabilities to predict interactions between bases, aiming to improve the accuracy of identifying potential TFBS. This research combines MegaDNA's model with long-range dependencies between bases to discover new and promising regulatory sites.

Read the original publication)