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

Jason Stajich jason.stajich at duke.edu
Thu Feb 23 13:29:57 EST 2006


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




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