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

Question

[geosmin]

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?

Answer 1

[5heikki]

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

[geosmin]

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

[5heikki]

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