Question: Extracting mRNA and protein Data from NCBI
0
gravatar for kevluv93
3.4 years ago by
kevluv93150
United States
kevluv93150 wrote:

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

blast sequence gene • 1.2k views
ADD COMMENTlink modified 3.4 years ago by alolex890 • written 3.4 years ago by kevluv93150
2
gravatar for alolex
3.4 years ago by
alolex890
United States
alolex890 wrote:

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.

ADD COMMENTlink written 3.4 years ago by alolex890

You saved my ass! Thank you!

ADD REPLYlink written 3.4 years ago by kevluv93150

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

ADD REPLYlink written 3.4 years ago by alolex890
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