[Bioclusters] Re: Help on BLAST

[Wim Glassee]

> > Recalculating the scores like this does create significant rounding
> > errors, mostly because of the number of significant digits in the
blast
> > output.
> 
> How significant is "significant" for your purposes? In my experience
with
> recombining BLAST reports, the errors introduced were rarely greater
than
> an order of magnitude.  Further, the erronious values seem to be
monotonic
> with the originals:  i.e, the list is in the same order.

Point taken. I take it you use this kind of merging yourself. Have you
had a change to think about my last question? About the differences in
-actual- results, hits and hsps. I've had differences on several
occasions.
E.g. a hit residing in the middle of a 5k subquery of a 100k query,
where blasting both gives different hsps in the smaller and the bigger
blast. I'd really like a second opinion on this.

> 
> E-values on individual hits vary more than an order of magnitude when
I
> update BLAST reports that are more than a year out of date against the
> public repositories.  They also vary slightly depending on the
bit-width
> (32 vs. 64) of the architecture I'm using.

Very interesting. Could the first case you state have anything to do
with the fact that the actual database is probably a lot bigger now than
when you first did your blast, which would naturally give a different
e-value.
The last case seems unavoidable.

Wim

PS Pretty productive mailing list!

> 
> I don't lose too much sleep trying to pass the "diff" test with my
BLAST
> reports.  It's a heuristic algorithm anyway.  I think that the time is
> more effectively spent giving my users access to another search
> methodology.
> 
> -Chris
> 
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