Entering edit mode
5.1 years ago
marongiu.luigi
▴
730
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
blastX or clustalX?
ops! it was BlastX...
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.
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?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.
Neither DB is equivalent to
nr
which is a superset of all available protein sequences.Why would you want to run an MSA tool on a BLAST database?
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)
If you were planning to do a protein search then may want to use
DIAMOND
instead ofblastx
. Not sure what your query sequence size is though.