How can I download the genomic sequence of multiple proteins in a single text file (FASTA)?

Question

[ysf.cyln]

Hi!

As you know, even if you only enter the accession number of hundreds of proteins in NCBI, it is possible to get both their peptide and cds sequences in a single file (text)? Is it possible to obtain the genomic sequence of these proteins in such an easy way?

[Ram]

Why not download separate files and cat them locally?

[GenoMax]

But you can surely get two files? One for nucleotides and one for protein? Post a few example accessions.

[ysf.cyln]

I will do it. Thank you.

Answer 1

[Aizan Fahri]

Hey,

Yes it is possible. I accomplish this by uploading a text file containing the accession ID. For example, I have these 3 genes below, 1 gene per line.

AGQ48050.1
AAA52724.1
AAD13886.1

And then, I upload it to the NCBI Batch Entrez (https://www.ncbi.nlm.nih.gov/sites/batchentrez). After uploading and hitting the Retrieve button, it would return a page search page. Make sure you choose the appropriate database (i.e. Protein, it defaults to Nucleotide) before querying!

Then, I would click the checkbox. Un-intuitively, there is a download all option but it is quite hidden. You need to click "Send to" (top right) after ticking all of the checkboxes, and then choose the download format that you need.