Waibhav Tembe wrote:
Hello List,
I understand that there are minor differences in e value computation
and the order in which hits with similar statistics/alignments are
reported
for blastall and mpiblast programs. Other than these two, are there any
significant differences in the outputs that need to be kept in mind
while comparing these two outputs?
As Michael mentioned, mpiblast prints the mpiblast paper reference.
that behaviour can be suppressed in 1.4 with the command-line switch
--altschul-reference
the e-value differences are truly miniscule and seem to be due to
floating point instability though I haven't had the patience to
definitively track it down.
the order of hits should be identical to that produced by NCBI blastall.
As far as I know, this info applies only to mpiBLAST 1.4.0 when used
with the Oct. 2004 toolbox. I personally have not thoroughly verified
it with any other toolbox release. NCBI doesn't provide a stable API
and things can change rather unexpectedly and significantly in their
toolbox. That said, I don't know of any reason why the output would be
different when using mpiblast with newer toolbox releases. Perhaps
somebody else knows whether anything is broken in newer releases?
-Aaron
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