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

Chris Fields cjfields at uiuc.edu
Thu Feb 23 13:34:19 EST 2006


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.
> >>>>
> >>>> 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
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> Bioperl-l mailing list
> >>>> Bioperl-l at lists.open-bio.org
> >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>
> >>>
> >>>
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> --
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12




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