FASTA-Fetcher: A Multicolumn Tool for Bulk Retrieval of NCBI Sequences in Plant-Biotic Stress Research

Timely and accurate detection of plant pathogens is critical for sustainable agriculture and forestry. Molecular methods enable unequivocal pathogen identification, especially when traditional diagnostics fall short, allowing timely and effective interventions. However, they rely on the large-scale retrieval of nucleotide sequences for robust phylogenetic analyses. Batch downloading from NCBI, however, remains a barrier for users without programming expertise. To address this challenge, in this chapter, we describe FASTA-Fetcher, a free, cross-platform, GUI-based application that automates large-scale sequence acquisition using NCBI accession numbers. Built on a lightweight, multithreaded Python framework, FASTA-Fetcher seamlessly integrates Biopython with NCBI's Entrez utilities to deliver responsive performance without freezing the GUI. All output files have undergone extensive validation to ensure compatibility with downstream programs such as MEGA, MAFFT, and BLAST. In usability trials, nonprogrammer participants reported effortless installation, intuitive operation, and consistent reliability. By lowering the technical barrier to bulk sequence retrieval, FASTA-Fetcher empowers researchers and students to incorporate high-throughput molecular workflows into their studies with confidence and ease.