Extracting mRNA and protein Data from NCBI

Question

[kevluv93]

Here's my problem: I want to get all of the mRNA and protein sequences for "pea aphid p450" off the NCBI database and into a textfile or FASTA so I can use them for analysis in other programs I have. I typed in "pea aphid p450" under "genes" and see that NCBI has all of the p450 sequences identified in pea aphids (there are 83 of them). I want to get all of this mRNA and protein data off of the NCBI website and into my computer. How would I go about doing that? I could just click on every accession number and copy and paste the mRNA and protein into a textfile, but I'm sure there's a better way.

Thank you and have a great day

Answer 1

[alolex]

See if these steps get you what you are looking for. You may have to filter the results though:

• After you pull up your 83 genes, look over to the right for the sidebar named "Find Related Data"
• Under Database select Nucleotide then Find Items
• I get 204 mRNA sequences. Click on Send To button at the top, select File, then choose FASTA format. Save the file.
• Go back to the nucleotide screen and click on Find Related Data again.
• This time select Protein and Find Items. I get 1827 protein sequences.
• Follow the Send To instructions to download all the protein sequences.

[kevluv93]

You saved my ass! Thank you!

[alolex]

Glad I could help :) Good luck with your research!