I've just found out that blast version 2.0.8 in psi-blast mode doesn't
recognize all hits that version 2.0.6 reported (though I used the same
parameters off course!).
In the README at ftp://ncbi.nlm.nih.gov/blast/executables/README it
Notes for 2.0.7 release:
2.) A problem with very redundant databases and psi-blast was fixed.
any idea what that means? My database shouldn't be redundant at all,
however I wonder whether the sequence found by version 2.0.6 with
e-value 1e-88 and %id 9.6 but not found in version 2.0.8 is due to the
mentioned change in version 2.0.7 ... .
Thanks for suggestions,
Biomolecular Modelling Laboratory
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