Downloading files is a fundamental task for bioinformaticians performing sequence alignment, comparative genomics, or phylogenetics. The NCBI RefSeq database provides a curated, non-redundant collection of genomic, transcript, and protein sequences.
The NCBI Datasets tool is the new standard for programmatic downloads, replacing older scripts. RefSeq: NCBI Reference Sequence Database refseq fasta download
For manual retrieval of specific sequences, the NCBI web interface is the most direct route. Use the NCBI search bar to find a specific gene or protein
If you have a list of Accession Numbers (e.g., NM_000546), use the Batch Entrez tool. Upload your list as a text file, retrieve the records, and then use the "Send to" menu to download them all in a single FASTA file. an entire genome
Use the NCBI search bar to find a specific gene or protein. From the results page, click the "FASTA" link. Use the "Send to" menu, select "File" , and choose "FASTA" as the format to save it to your computer.
For entire genomes, go to the Assembly database. Locate your species and use the "Download Assemblies" button to select RefSeq as the source and FASTA as the file type. 2. NCBI Datasets CLI (Recommended for Modern Workflows)
Depending on whether you need a single gene, an entire genome, or a massive batch of sequences, there are three primary methods to download RefSeq FASTA data. 1. Web Browser Downloads (Single or Small Sets)