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

Raghunath Verabelli iamvela at yahoo.com
Thu Feb 23 14:33:50 EST 2006


Chris, you are right. I am using NCBI BLAST.

Here is my http query:

my $urltext =
"http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Put&QUERY=$seq&DATABASE=nr&PROGRAM=blastp";

This is my code for populating p-value:

my $pValue = $bioPerlHit->significance;


I looked at the text output, could not find any p
value column, the only 'value' column in the output is
'E value'. I will try that.

Thanks,
Raghu
 
--- Chris Fields <cjfields at uiuc.edu> wrote:

> I think Raghu's running NCBI BLAST, though.  Am I
> right? 
> 
> Christopher Fields
> Postdoctoral Researcher - Switzer Lab
> Dept. of Biochemistry
> University of Illinois Urbana-Champaign 
> 
> 
> > -----Original Message-----
> > From: Jason Stajich
> [mailto:jason.stajich at duke.edu]
> > Sent: Thursday, February 23, 2006 12:30 PM
> > To: Chris Fields
> > Cc: 'Raghunath Verabelli';
> bioperl-l at lists.open-bio.org
> > Subject: Re: [Bioperl-l] Blast returns result, but
> does not return hits
> > 
> > p-values do show up in WU-BLAST reports so that is
> why we have a p-
> > value function.
> > 
> > 
> > On Feb 23, 2006, at 1:06 PM, Chris Fields wrote:
> > 
> > > 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.
> > >>>>
> 
=== message truncated ===


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