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Running blastX locally

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

sequencing alignment clustalx local database
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updated by Asaf Asaf • written by marongiu.luigi marongiu.luigi

blastX or clustalX?

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written by Asaf Asaf

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.

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written by Ram Ram

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?

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written by marongiu.luigi marongiu.luigi

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.

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written by Ram Ram

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

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written by GenoMax GenoMax

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

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written by Joe Joe

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)

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written by lieven.sterck lieven.sterck

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.

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written by GenoMax GenoMax

1 answer

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

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written by Asaf Asaf

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