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

[Bhakti Dwivedi]

Thanks Chris!  I changed few parameter values in blastcl3 and now the
results are same.  Any particular reason to set the default differently in
web-based and command-line blast search?

Bhakti



On Mon, May 10, 2010 at 12:28 PM, Chris Fields <cjfields at illinois.edu>wrote:

> 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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>