NCBI BLAST standalone database in other folder

Question

[philipp]

Hi everyone,

I have a rather simple question but did not find a working answer. I have the BLAST standalone software on my computer and so far I had all databases that I use in the */bin folder. I want to use the huge RefSeq database now and I have to save the database on a external hard drive. Is there a way to adjust the command in a way that it looks for the database in a folder other than the standard */bin folder?

Thanks for your help!

Best, Philipp

[st.ph.n]

with the -db parameter, specify the path to the database (after running makeblastdb)

[philipp]

Ok, thanks. I appreciate your input. Could you please describe in a bit more detail how to specify the path? Or do you have an example or know a tutorial where that is described?

[GenoMax]

What OS are you running this on? If linux, then it can be simply be export BLASTDB=/path_to/refseq_index_files.

[Sej Modha]

http://bioinformatics.cvr.ac.uk/blog/setting-up-automatic-blast-database-update-on-linux-servers/

Answer 1

[GenoMax]

You can set a variable BLASTDB to point to that external drive (location of the index file folder). This would be a less than optimal solution in terms of speed but you are probably aware of that.

Please don't use any spaces in the names anywhere since that can only lead to trouble.