I have a crazy problem where I run blastn of a test sequence against a database on the command line and get no results, but when I run it through SequenceServer (using the same blast database and blast program), I get a fantastic hit.
I did notice that the blastn matrix is 2 -3 on the SServer output, and 1 -2 on my default blast output, and gapopen and gapextend are also different. However, changing these in my command line run doesn’t help. Maybe it’s a repeat mask issue (though I don’t see any repeats)…? In any case, what is the exact blast command inside the bowels of SServer?