SeqFetcher

Input

Start with one ID or a whole list.

Up to 500 IDs

Accession numbers or UIDs

ⓘ Separate IDs with newlines, commas, spaces, or semicolons. Duplicates are removed. Files should contain IDs only, without a column header.

Configure retrieval

NCBI databaseNucleotideDNA and RNA · RefSeq / GenBankATGCProteinAmino acid sequences · RefSeq / GenPeptMKWV

IDs per request

Use sequence accessions, numeric sequence UIDs, or GCA_/GCF_ genome assemblies with Nucleotide selected. Assemblies are fetched one at a time. Gene, Taxonomy, BioProject, and SRA IDs are not supported.

Review and download

Your sequences will appear here

	Accession / Input ID	Organism and description	Length	Status	Actions

0 records selected

Keep the private job link to return to saved results after closing or refreshing.

A QUICK GUIDE

Which IDs can I use?

Use nucleotide accessions such as NM_000546.6 or NC_012920.1, protein accessions such as NP_000537.3, or numeric sequence UIDs from the chosen database. For whole genomes, select Nucleotide and use an assembly accession such as GCA_033896045.1 or GCF_000339015.1. All chromosomes and contigs are returned as separate FASTA records. An accession without a version retrieves the current version. Gene symbols and Gene IDs require a different lookup and are not supported here.

What is included in my download?

FASTA exports contain each selected sequence once. ZIP includes a combined FASTA, individual sequence files, selected metadata in TSV and JSON, a complete run report, and failed / pending ID lists. Metadata includes organism, taxonomy, sequence length, and the original NCBI link.

Working with large batches or genomes?

The page accepts up to 500 unique IDs and retains up to 25 MB of FASTA output. Each request also has a limit of 8 million bases or amino-acid residues. Choose one ID per request for larger records; a single record above this limit still requires the CLI. Assembly accessions automatically use one ID per request. For larger jobs, create a UTF-8 file named ncbi_ids.txt with one ID per line, then run python ncbi_fetch.py --id-file ncbi_ids.txt --out ncbi_batch --zip from the project directory. Use python ncbi_fetch.py --help for script options.

Why did a record fail?

Check the selected database and accession version. WGS master records may not contain a downloadable sequence. Retry failed or pending IDs as a new job; the original job keeps its successful records. Stop allows the current batch to finish and leaves the remaining IDs pending. Keep the private link to restore saved results from My Jobs.