[Bioperl-l] Bio::Search::Hit

[Mike Muratet]

On Thu, 7 Apr 2005, Jason Stajich wrote:

> It should give you whatever is in your BLAST report - only one is 
> reported in the Hit table at the top of the report....
> 
> Default WU-BLAST settings gives you p-values for Hit table while 
> NCBI-BLAST gives you E-values.  For HSPs, one can get p-value with p() 
> and evalue with evalue().
> 
> 
> -jason

Jason

Thanks. I wasn't aware of the difference.

mike

> --
> Jason Stajich
> jason.stajich at duke.edu
> http://www.duke.edu/~jes12/
> 
> On Apr 7, 2005, at 9:27 AM, Mike Muratet wrote:
> 
> > Greetings
> >
> > I have use the 'significance' method in Bio::Search::Hit (and other
> > objects) to parse blast results into a mysql database. I just went 
> > back to
> > the documentation to determine if it returns 'e' or 'p' and it says 
> > only
> > that it returns one or the other. Does anyone know for sure which one 
> > it
> > is (given that they are numerically equivalent for small values)?
> >
> > Thanks
> >
> > mike
> >
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> 
>