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How do I download and set up a subset of a local database from NCBI?

I want to use blast+ on a local preformatted database from NCBI using:

update_blastdb.pl --decompress nr

However, since I don't have that much space on my computer I just want to download a subset of sequences (e.g. limited to cyanobacteria). Is it possible to include this in the command?

Also I was wondering if it would be better to download the genomes and instead perform a blastx search on the complete genome? Would I set this up downloading the nt database?

blast+ ncbi local database
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updated by 5heikki 5heikki • written by geosmin • geosmin

1 answer

You can parse Cyanobacteria genome NCBI ftp urls from this file and then use a tool like wget or curl to download the genomes. Then you make your Cyanobacteria db with the makeblastdb command

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written by 5heikki 5heikki

Thank you! I can't open the link though. Could you explain how did you get to this summary?

• 0 views • link
written by geosmin • geosmin

Don't try to open the link, it's a huge file and will most likely freeze your browser. Just download the file instead..

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written by 5heikki 5heikki

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