[Bioperl-l] Different Blast results from web-based interface and command line interface

[Bhakti Dwivedi]

Does anyone know why the blast results vary for a query sequence when search
is conducted using a web-based interface versus a Command line interface?

For example, my web-based blast top hits do not match  the top hits of the
command line blast (blastcl3).  I am using the default settings in both.
not sure why the results are different  Even if the hit is there, the
e-value, bit score etc are different for the same hsp regions identified
within the hit.  is there a difference in the blast algorithm?  or is it the
database?

Thanks!