[Bioperl-l] Blast returns result, but does not return hits

Thu Feb 23 18:06:37 UTC 2006

Hold up a second.  Do you mean e-value, or p-value?  A run-of-the-mill NCBI
blast report these days gives e-values (expectation value), NOT p-values.  I
think they changed over to using only e-values with BLAST v2.  Make sure you
didn't mix these up; look out the text output to make sure that P values are
present.  That would explain why you're getting 0, since they don't exist.

>From the BLAST tutorial:

The BLAST programs report E-value rather than P-values because it is easier
to understand the difference between, for example, E-value of 5 and 10 than
P-values of 0.993 and 0.99995. However, when E < 0.01, P-values and E-value
are nearly identical.

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Chris Fields
> Sent: Thursday, February 23, 2006 11:41 AM
> To: 'Raghunath Verabelli'; bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Blast returns result, but does not return hits
> 
> Yes that's a potential issue.  I'll try to replicate that here; please
> send
> a code example so I can see how you're calling for the p-value.
> 
> Christopher Fields
> Postdoctoral Researcher - Switzer Lab
> Dept. of Biochemistry
> University of Illinois Urbana-Champaign
> 
> > -----Original Message-----
> > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> > bounces at lists.open-bio.org] On Behalf Of Raghunath Verabelli
> > Sent: Thursday, February 23, 2006 10:24 AM
> > To: Chris Fields; bioperl-l at lists.open-bio.org
> > Subject: Re: [Bioperl-l] Blast returns result, but does not return hits
> >
> > Thanks Chris for all your help.
> >
> > The patch for blast.pm worked. I was able to parse the
> > hits from the raw file. I uninstalled previous
> > versions of bioperl using ppm and then I installed
> > bioperl 1.4.x using nmake, and applied your fix. I am
> > getting hits the way I wanted.
> >
> > However, I noticed that the p-value for each hit
> > doesn't seem to be parsed
> > correctly. It sets it to 0 for all hits. Not sure if
> > this is a known issue. Any suggestions/comments,
> > please let me know.
> >
> > Thanks,
> > Raghu
> >
> > --- Chris Fields <cjfields at uiuc.edu> wrote:
> >
> > > > -----Original Message-----
> > > > From: bioperl-l-bounces at lists.open-bio.org
> > > [mailto:bioperl-l-
> > > > bounces at lists.open-bio.org] On Behalf Of Raghunath
> > > Verabelli
> > > > Sent: Wednesday, February 22, 2006 8:25 PM
> > > > To: Chris Fields; bioperl-l at lists.open-bio.org
> > > > Subject: Re: [Bioperl-l] Blast returns result, but
> > > does not return hits
> > > >
> > > >
> > > > Thanks very much Chris for your time.
> > > > Please see below output that you requested (the
> > > only
> > > > difference i saw between your output and mine is
> > > @INC
> > > > value. I have only 2 directories c:\mod_perl\perl
> > > > where i installed activeperl. I see two additional
> > > > directories in your @INC path).
> > > >
> > > > >
> > > > > When you type 'perl -V' what do you see (make
> > > sure
> > > > > it is a capital 'V', not
> > > > > lower case).
> > > >
> > > > C:\Documents and Settings\Administrator>perl  -V
> > > > Summary of my perl5 (revision 5 version 8
> > > subversion
> > > > 7) configuration:
> > > >   Platform:
> > > >     osname=MSWin32, osvers=5.0,
> > > > archname=MSWin32-x86-multi-thread
> > >
> > > [....]
> > >
> > > > if.pm
> > > >   Built under MSWin32
> > > >   Compiled at Nov  2 2005 08:44:52
> > > >   %ENV:
> > > >     PERL5LIB="c:\bioperl-live"
> > > >   @INC:
> > > >     c:\bioperl-live
> > > >     C:/mod_perl/Perl/lib
> > > >     C:/mod_perl/Perl/site/lib
> > > >     .
> > >
> > > Personally I wouldn't place the the bioperl-live
> > > folder in the root
> > > directory; this shouldn't make a difference, but you
> > > can try moving it to
> > > the perl directory in a separate folder to see if
> > > that helps.  Can't see why
> > > it would make a difference, but it is Windows...
> > > Main reason I'll switching
> > > over to Mac OS X!
> > >
> > > Make sure that the Bio directory is in the
> > > bioperl-live directory,
> > > regardless (i.e. if PERL5LIB is set to
> > > C:\mod_perl\Perl\bioperl\bioperl-live, then there
> > > should be a directory like
> > > C:\Perl\bioperl\bioperl-live\Bio).  Otherwise it
> > > won't work.
> > >
> > > What do you get with this?
> > >
> > > perl -MBio::Root::Version -e "print
> > > $Bio::Root::Version::VERSION"
> > >
> > > If everything is working (PERL5LIB, etc) then it
> > > should be 1.5 for CVS
> > > bioperl; otherwise it will either find the old
> > > version (1.2.3) or fail
> > > completely.
> > >
> > > Christopher Fields
> > > Postdoctoral Researcher - Switzer Lab
> > > Dept. of Biochemistry
> > > University of Illinois Urbana-Champaign
> > >
> > >
> > > _______________________________________________
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> > > Bioperl-l at lists.open-bio.org
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> > >
> >
> >
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