Entering edit mode
8 weeks ago
fafad046 • 0
I have a list of NCBI protein accession numbers from multiple organisms.
- What is the best way to get their corresponding intron positions for each amino acid sequence?
My current idea is to download all of their DNA sequences from NCBI and compare them with their corresponding mRNA sequences, but I also had trouble finding their corresponding DNA sequences from the protein accession number itself, which leads to my second followup question:
- How do I get DNA accession numbers from my protein accession numbers on the NCBI website?
- Alternatively is there any databases where I can get both the protein sequences and intron position more cleanly?
Any input is greatly appreciated, thank you!
thank you so so much, it worked! you are an absolute life savior :D
Do you happen to know why sometimes my Entrez direct command gives no output at all?
I installed Entrez direct using the commands listed on the website:
Then, my below command sometimes gives my desired output (all the gene tables corresponding to that protein ID), but now it doesn't give any output at all.
Im really hoping that it'd work as it has been such a convenient tool, thank you so much in advance..
Did you sign up for NCBI_API_KEY? This is a public resource so if you are doing a large number of queries put a pause between query blocks. Even with NCBI API Key you are allowed a certain number of queries per unit time.
The query above does work.