Question: (Closed) Bioinformatics: Create organism specific local database
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gravatar for tom5
7 months ago by
tom50
tom50 wrote:

I am trying to run protein BLAST alignment locally through BLAST+ and want to download the nr database. However, due to the large size of the database, I'd like to only download the portion of the dataset that corresponds to organisms I am working with: Mouse and chicken.

I looked at the NCBI guide and it gives a command to download databases: update_blastdb.pl --decompress nr [*]

However, I am not sure how to specify an organism specific download. Please let me know if you have a recommendation. Have a good evening.

blast database ncbi • 143 views
ADD COMMENTlink written 7 months ago by tom50

Hello tom5!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

PS: Please keep it focused in one thread.
ADD REPLYlink written 7 months ago by ATpoint42k

You are best off downloading mouse and chicken genome fasta files from NCBI datasets and then creating the database yourself. You can't download organism specific subsets of nr database.

ADD REPLYlink written 7 months ago by GenoMax93k
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