MAFFT #2 MAFFT 실행 #

#2025-07-28

1. Objective #

Influenza의 Reference squence는 길이가 fix되어있지만,

각 sequence는 삽입/탈락 mutation이 일어남에 따라 모두 길이가 같지 않다.
이 길이를 맞춰주는 padding을 하기 위해 MAFFT를 이용해 정렬(Multiple Sequence Alignment)한다.

#

2. MAFFT 실행 bash script #

#data

/Influenza
└── Preprocessed/
     ├── HA/
     │    ├── A-H1N1.fasta
     │    ├── A-H1N1.fasta
     │    ├── ...
     │    └── B.fasta
     └── ...
          └── (HA와 동일 구조)
└── MAFFT/
     └── (empty)

#!/bin/bash

# List of genes and files to process
gene_list=('HA' 'NA' 'MP' 'PA' 'NS' 'PB1' 'PB2' 'NP')
file_list=('A-H1N1' 'A-H3N2' 'A-H5N1' 'B')

# Loop through each gene and file
for gene in "${gene_list[@]}"; do
    echo "Processing gene: $gene"
    
    for file in "${file_list[@]}"; do
        echo "Processing file: $file"
        
        # Define directories and file paths
        input_fasta="/data3/projects/2020_MUTCLUST/Data/Projects/GISAID_revision/Influenza/Preprocessed/${gene}/${file}.fasta"
        reference_fasta="/data3/projects/2020_MUTCLUST/Data/Projects/GISAID_revision/Influenza/Reference/Preprocessed/${gene}/${file}.fasta"
        output_dir="/data3/projects/2020_MUTCLUST/Data/Projects/GISAID_revision/Influenza/MAFFT/${gene}"
        output_fasta="${output_dir}/${file}.fasta"
        
        # Create output directory if it doesn't exist
        mkdir -p "$output_dir"
        
        # Perform multiple sequence alignment with MAFFT
        echo "Running MAFFT for ${gene}/${file}..."
        mafft --thread 50 --anysymbol --add "$input_fasta" --keeplength "$reference_fasta" > "$output_fasta"
        
        # Check if MAFFT was successful
        if [ $? -eq 0 ]; then
            echo "Alignment complete: $output_fasta"
        else
            echo "MAFFT alignment failed for ${gene}/${file}"
        fi
    done
done

#result

/Influenza
└── Preprocessed/
     ├── HA/
     │    ├── A-H1N1.fasta
     │    ├── A-H1N1.fasta
     │    ├── ...
     │    └── B.fasta
     └── ...
          └── (HA와 동일 구조)
└── MAFFT/
     ├── HA/
     │    ├── A-H1N1.fasta
     │    ├── A-H1N1.fasta
     │    ├── ...
     │    └── B.fasta
     └── ...
          └── (HA와 동일 구조)