Question: How can I download the genomic sequence of multiple proteins in a single text file (FASTA)?
0
gravatar for ysf.cyln
7 months ago by
ysf.cyln0
Turkey
ysf.cyln0 wrote:

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?

sequence assembly • 322 views
ADD COMMENTlink modified 7 months ago • written 7 months ago by ysf.cyln0

Why not download separate files and cat them locally?

ADD REPLYlink written 7 months ago by RamRS30k

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

ADD REPLYlink written 7 months ago by genomax92k

I will do it. Thank you.

ADD REPLYlink written 7 months ago by ysf.cyln0
0
gravatar for Aizan Fahri
7 months ago by
USA/Rochester/URMC
Aizan Fahri0 wrote:

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.

Send to

ADD COMMENTlink written 7 months ago by Aizan Fahri0
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