I'm confused on BLAST file formats and somewhat on the BLAST tool
structure itself. I have no experience with BLAST, but I recognize
BLAST can read several input formats including FASTA.
Assume I'm using the latest version of BLAST. It seems to me there
would be three file stages. First would be the input files to be
processed with some heuristical program. Second would be the output
files from that tool; these output files would also be the input files
to a tool that would produce the exact alignment. So the third stage
files would be the alignment files themselves. Is that even remotely
close to reality?
What I really want to know is the file format of the stage two files --
the output of the BLAST tools before they do the sequence alignment.
Where do I get that information?