How can I bulk download transcript sequences?

Question

[david.f.stein]

I have a list of NCBI transcript accessions. I would like to download the sequences for these transcripts in fasta format or any format that is available so that I can run the sequences through RNA folding sotware. Does anyone know of a repository from which I can query and download these sequences?

[GenoMax]

You can also use EntrezDirect if you prefer a command line option. (LINK)

For example:

$ cat acc.txt

XM_022318843
XM_022318845
XM_022328847

$ epost -db nuccore -input acc.txt -format acc | efetch -format fasta > file.fa

[david.f.stein]

Oh nice this works too, thanks!

Answer 1

[grant.hovhannisyan]

https://www.ncbi.nlm.nih.gov/sites/batchentrez

[david.f.stein]

Fantastic, this is exactly what I needed. Thanks!