Hi. I'm new to blast. I have downloaded blast+ and installed on a windows machine.
I want to use blast to align short nucleotide sequences (<400 bases) A against reads of similar length B. Set A and B are only tens of reads each.
I see that I can use formatdb on one set of reads (A) and then use blast+ to match my other set of reads (B).
This is acceptable, but I see that NCBI hosts a tool where you can blast two sequences. Is this possible with the standalone blast without building the database?
Not sure it matters, but I'm doing this on windows, probably with a python wrapper.