> The GenBank BLAST Email Server uses defaults of 5 and -4 for parameters
> M and N in blastn jobs.
I see that NCBI has a response to your question further down
in the header list for items in this newsgroup. I just want to
clarify that GenBank has not added anything to the BLAST program
itself nor changed its default values. The version of BLAST used on
the GOS e-mail server can also be FTPed from ncbi.nlm.nih.gov if you
want to fiddle around with reformating the databases locally. The
only "added value" that we at GenBank provide are the e-mail access
and the database maintenance. I am happy to see that the folks at
NCBI have posted a theoretical explanation of the parameter because
they as authors of the program are obviously best suited to do so.
kristoff at genbank.bio.net