Running blastX locally

Question

[marongiu.luigi]

Hello

is it possible to run blastX on a local database? If I download the entire database with update_blastdb.pl as shown in this post, would blastX work? I need to do this because in remote it takes too long to run. Locally I will need the space for the files but I will save in time, I guess.

Also, shall I use bot nr and nt databases?

Thank you

[Asaf]

blastX or clustalX?

[marongiu.luigi]

ops! it was BlastX...

[Ram]

If your local database is a protein database, blastx should work fine. nr is the database you're looking for.

EDIT: I thought nr was a nucleotide database just like nt, but I was mistaken.

[marongiu.luigi]

from the manual, they cite swissprot: ./update_blastdb.pl --decompress swissprot; is there another database I should duse to get the equivalent of nr/nt for the proteins?

[Ram]

swissprot is also a protein, although you might want to look at trembl as well. IIRC, Swissprot is manually curated whereas trembl includes translated-from-nucelotide proteins as well.

[GenoMax]

Neither DB is equivalent to nr which is a superset of all available protein sequences.

[Joe]

Why would you want to run an MSA tool on a BLAST database?

[lieven.sterck]

only nr is applicable for BlastX (nucleo vs protein comparison)

Keep in mind that nowadays with the size of nr it will also take a very long time running it locally, unless you have access to a large and powerful HPC system. (I would personally NOT advise to run this locally on a lap or desktop machine)

[GenoMax]

If you were planning to do a protein search then may want to use DIAMOND instead of blastx. Not sure what your query sequence size is though.

Answer 1

[Asaf]

Yes, you can use BlastX locally. Since BlastX search a translated DNA vs a protein dataset you will need to download nr (the protein dataset). nt is useful for BlastN (DNA-DNA match).

Good luck