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

[Chris Fields]

The default web-based parameters differ than those via blastcl3, so if you are using the defaults for both they may differ somewhat.

chris

On May 10, 2010, at 10:22 AM, Bhakti Dwivedi wrote:

> 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!
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