I would like to blast two databases of around 50,000 sequences each against one another. Is there a way to do this?
I would like to blast two databases of around 50,000 sequences each against one another. Is there a way to do this?
Blasting two databases
I assume you mean two sets of sequences since databases can't be blasted against each other.
This can be easily done using blat
(LINK Jim Kent from UCSC) or blast+
if you prefer that. With blat
you would not need to create database indexes, just search with one file against the other. With blast+
you will need to create indexes for one and use that as the database to search against.
Use a tabular output format like 6
or 7
to make parsing easier later.
Note: blat
would be useful only if your sequences are reasonably similar. If they are not then you should use blast+
.
You can do a reciprocal blast search (which I think is intended here) using a tool like proteinortho https://www.bioinf.uni-leipzig.de/Software/proteinortho/
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.