Re: forcing a full sequence comparison in blast

Hi, Phil!

> Is there a way I can force blast to use the full 347 amino acids for
> comparison.

No. It does not make sense to put sequences into an alignment that do not
belong together.

> The researchers in my lab are most interested in places
> with low similarities, since they are trying to find the portions
> which make this organism virulent.

Blast can create output in form of a table. Or you can choose the output
option XML and convert that into a table. You can filter this table for
genes which made only a bad hit. Where "bad" would have to be defined
carefully.

Then determine which genes did not make a blast hit at all.

That way you would get a set of candidate genes causing virulence. (As far
as this is possible with this kind of analysis.)

Greetings from Germany,
Michael.