[Bioperl-l] bioperl 1.4 SearchIO doesn't work parsing blast output

Pieter Monsieurs Pieter.Monsieurs at esat.kuleuven.be
Fri Feb 10 03:53:43 EST 2006


Hi Chris,

The parsing of the Blast output still doesn't work for me with the bug 
fix download of blast.pm.
The module keeps turning around in the while loop at line 487 looking 
for a database or query-size:

while( defined ($_) ) {
	if( /^Database:/ ) {
		$self->_pushback($_);
		last;
	}
	chomp;               
	if( /\((\-?[\d,]+)\s+letters.*\)/ || /^Length=(\-?[\d,]+)/ ) {
		$size = $1;
		$size =~ s/,//g;
		last;
	} else {
		$q .= " $_";
		$q =~ s/ +/ /g;
		$q =~ s/^ | $//g;
	}
	$_ = $self->_readline;
}


The code keeps looking for the database information, however - as you 
mentioned - this information is given before the query line in the new 
Blast output format.
This way, all hits and hsps are stored in the query_description 
($hit->query_description), no hits are found and query_length is 0.
Because you already adapted the module to retrieve database information 
at another position in the module, deleting the while loop and adding 
the following lines after $_ = $self->_readline (line 486), worked fine 
for me (using blastn and blastp):

if (/Length=([\d,]+)/) {
	$size = $1;
	$size =~ s/,//g;
}


Regards,
Pieter



Chris Fields wrote:

> From 'perldoc Bio::SearchIO::blast':
>
>DESCRIPTION
>        This object encapsulated the necessary methods for generating  
>events
>        suitable for building Bio::Search objects from a BLAST report  
>file.
>        Read the Bio::SearchIO for more information about how to use  
>this.
>
>        This driver can parse:
>
>        o   NCBI produced plain text BLAST reports from blastall,  
>this also
>            includes PSIBLAST, PSITBLASTN, RPSBLAST, and bl2seq  
>reports.  NCBI
>            XML BLAST output is parsed with the blastxml SearchIO driver
>
>        o   WU-BLAST all reports
>
>        o   Jim Kent's BLAST-like output from his programs (BLASTZ,  
>BLAT)
>
>        o   BLAST-like output from Paracel BTK output
>
>So, it should.  Let us know if it doesn't.
>
>On Feb 9, 2006, at 4:20 PM, Hubert Prielinger wrote:
>
>  
>
>>Hi Chris,
>>I'm incredibly sorry for causing so much inconvenience, yes you are  
>>right, I had only to change the blast.pm file, it is working very  
>>fine, thank you very much, and you are right, you have mentioned it  
>>ealier either to change the file... ;)
>>
>>but I have another question: does it work with the WU-Blast output  
>>too?
>>regards
>>Hubert
>>
>>
>>Chris Fields wrote:
>>
>>    
>>
>>>Ha!  I come back from meeting and there's a billion emails!  What  
>>>have we
>>>started? ;p .  Sorry about this Jason; I know you're busy.
>>>
>>>Hubert, if you're out there, I sent you an email with an  
>>>attachment.  You
>>>said the output looks like what you were expecting.  So I think we  
>>>have two
>>>problems:
>>>
>>>1)  I haven't delved into the file scanning, but the fact that it  
>>>takes so
>>>long should tell you something's seriously wrong there.  Strip  
>>>that part out
>>>and start with a simple script, say, like the one Jason or that I  
>>>sent you;
>>>the script I used to generate that output works fine (on two OS's,  
>>>WinXP and
>>>Mac OS X).  Use it on one file at a time.  Do everything on  
>>>command line
>>>(not through Eclipse).  IDE's can be notoriously flaky about running
>>>scripts, esp. when they run debugging.
>>>2) Even if you have bioperl-1.5.1 installed, Bio::SearchIO::blast  
>>>will still
>>>not work whenever the text blast output has the following header,  
>>>which
>>>comes from the new web version of BLAST:
>>>
>>>-----------------------------------------------------
>>>BLASTP 2.2.13 [Nov-27-2005]
>>>Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A.  
>>>Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J.  
>>>Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of  
>>>protein database search programs", Nucleic Acids Res. 25:3389-3402.
>>>
>>>RID: 1139501210-857-165793005128.BLASTQ1
>>>
>>>
>>>Database: All non-redundant GenBank CDS
>>>translations+PDB+SwissProt+PIR+PRF excluding environmental samples
>>>          3,292,813 sequences; 1,128,164,434 total letters
>>>Query=  NP_215895 pyrimidine regulatory protein PyrR [Mycobacterium
>>>tuberculosis H37Rv].
>>>Length=193
>>>.......
>>>-----------------------------------------------------
>>>
>>>It will work if the text output has the following header (or is an  
>>>older
>>>version of BLAST):
>>>
>>>-----------------------------------------------------
>>>BLASTP 2.2.12 [Aug-07-2005]
>>>
>>>
>>>Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A.  
>>>Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J.  
>>>Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of  
>>>protein database search
>>>programs",  Nucleic Acids Res. 25:3389-3402.
>>>
>>>Query= NP_215895 pyrimidine regulatory protein PyrR [Mycobacterium
>>>tuberculosis H37Rv].
>>>        (193 letters)
>>>
>>>Database: All non-redundant GenBank CDS
>>>translations+PDB+SwissProt+PIR+PRF excluding environmental samples
>>>          2,895,325 sequences; 997,103,285 total letters
>>>-----------------------------------------------------
>>>You have the former (2.2.13) version.  I know b/c I have your  
>>>BLAST files.
>>>Therefore, even bioperl-1.5.1 will not work!
>>>
>>>If you want the really gory details on why this is a problem, look  
>>>here:
>>>
>>>http://bugzilla.bioperl.org/show_bug.cgi?id=1934
>>>
>>>So, any text output with the above header will not work; it will  
>>>either hang
>>>or end abruptly (depending on OS, perl version, memory,  
>>>patience).  If you
>>>look in the above, I have added a preliminary fix for this.  I'll  
>>>reiterate
>>>for the billionth time, it hasn't been committed yet, so don't  
>>>kill me if
>>>blows your computer up ;>
>>>Here's the direct link:
>>>http://bugzilla.bioperl.org/attachment.cgi?id=267&action=view
>>>This is a modified version of Bio::SearchIO::blast.pm (it says  
>>>it's version
>>>1.90, but it's lying, I didn't change the version, only the regex;  
>>>sorry
>>>Jason).  From what you've been posting it doesn't sound like  
>>>you've tried
>>>this, and I believe I've suggested this fix before.
>>>
>>>Replace the one in your Bio/SearchIO directory (which looks like
>>>'/usr/lib/perl5/site_perl/5.8.6/Bio/SearchIO/', judging from your  
>>>prev.
>>>message) with this file.  Make sure the filename stays the same  
>>>(blast.pm).
>>>
>>>Run everything again, one file at a time.  Make sure you use  
>>>Jason's script
>>>as well as the one I sent you.  Do NOT rely on running through  
>>>multiple
>>>files yet.  Fix one bug at a time.  And heed Joel's words about  
>>>file checks.
>>>
>>>
>>>Here's a small chunk of output from one of your blast files using the
>>>modifed script I sent you:
>>>
>>>sp|Q10264|PSO2_SCHPO-->DNA cross-link repair protein pso2/snm1
>>>Query:   1  RWKWKRKK  8
>>>Seq:     542  RWAWRRKK  549
>>>
>>>Look familiar?
>>>
>>>Christopher Fields
>>>Postdoctoral Researcher - Switzer Lab
>>>Dept. of Biochemistry
>>>University of Illinois Urbana-Champaign
>>>
>>>      
>>>
>>>>-----Original Message-----
>>>>From: Roger Hall [mailto:rahall2 at ualr.edu] Sent: Thursday,  
>>>>February 09, 2006 3:24 PM
>>>>To: 'Hubert Prielinger'; 'Chris Fields'; 'Jason Stajich'
>>>>Subject: RE: [Bioperl-l] bioperl 1.4 SearchIO doesn't work  
>>>>parsing Blast output
>>>>
>>>>In other words, yes, I'm on the wrong trail. :}
>>>>
>>>>Sorry - I'll look at the output issue this evening (or realize  
>>>>that Chris already solved the issue).  ;}
>>>>
>>>>Thanks!
>>>>
>>>>Roger
>>>>
>>>>-----Original Message-----
>>>>From: bioperl-l-bounces at lists.open-bio.org
>>>>[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hubert  
>>>>Prielinger
>>>>Sent: Thursday, February 09, 2006 2:14 PM
>>>>To: rahall2 at ualr.edu; bioperl-l at bioperl.org; Chris Fields; Jason  
>>>>Stajich
>>>>Subject: Re: [Bioperl-l] bioperl 1.4 SearchIO doesn't work  
>>>>parsing Blast output
>>>>
>>>>dear roger,
>>>>this error message I got, when I tried to parse Blast output  
>>>>(version
>>>>2.2.12) with bioperl 1.5.1, but it doesn't matter, because I have  
>>>>a lot of Blast output files with version 2.2.13 and for that I  
>>>>don't get any error message.....it just doesn't work
>>>>
>>>>Hubert
>>>>
>>>>
>>>>
>>>>Roger Hall wrote:
>>>>
>>>>
>>>>        
>>>>
>>>>>Guys - I'm looking at the error message:
>>>>>
>>>>>MSG: no data for midline Query  1   WWWKWRW  7
>>>>>STACK Bio::SearchIO::blast::next_result
>>>>>/usr/lib/perl5/site_perl/5.8.6/Bio/SearchIO/blast.pm:1151
>>>>>STACK toplevel
>>>>>/home/Hubert/installed/eclipse/workspace/Database_Search/ 
>>>>>Blast.pl:21
>>>>>
>>>>>This is my line of thought:
>>>>>1. "no data for midline $_" is a unique message generated by
>>>>>          
>>>>>
>>>>blast.pm
>>>>        
>>>>
>>>>>in
>>>>>
>>>>>          
>>>>>
>>>>one
>>>>
>>>>        
>>>>
>>>>>location only at the point of a. reading three lines b.
>>>>>          
>>>>>
>>>>dropping lines
>>>>        
>>>>
>>>>>with spaces only c. identifying the Query, Midline, and
>>>>>          
>>>>>
>>>>Match lines (0
>>>>        
>>>>
>>>>><= $i <
>>>>>
>>>>>          
>>>>>
>>>>3)
>>>>
>>>>        
>>>>
>>>>>2. There is a regexp match that fails in order to reach that
>>>>>          
>>>>>
>>>>error message
>>>>
>>>>        
>>>>
>>>>>3. The $_ value "Query  1   WWWKWRW  7" should not fail the
>>>>>          
>>>>>
>>>>expression
>>>>
>>>>        
>>>>
>>>>>4. It does anyway
>>>>>5. I cannot find the value "Query  1   WWWKWRW  7" anywhere
>>>>>          
>>>>>
>>>>in the blast
>>>>
>>>>        
>>>>
>>>>>reports
>>>>>
>>>>>I suspect a newline/chomp/metacharacter issue. Not finding
>>>>>          
>>>>>
>>>>the string
>>>>        
>>>>
>>>>>anywhere has me thoroughly confused - I asked Hubert for the
>>>>>          
>>>>>
>>>>additional
>>>>        
>>>>
>>>>>file, assuming that I didn't have it.
>>>>>
>>>>>My next thought is to write a quick script to test perl behavior  
>>>>>on "Fedora Core 9".
>>>>>
>>>>>Thoughts?
>>>>>
>>>>>Did I misread the issue entirely? :}
>>>>>
>>>>>Roger
>>>>>
>>>>>
>>>>>-----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 09, 2006 10:16 AM
>>>>>To: 'Jason Stajich'; 'Hubert Prielinger'
>>>>>Cc: bioperl-l at bioperl.org
>>>>>Subject: Re: [Bioperl-l] bioperl 1.4 SearchIO doesn't work  
>>>>>parsing Blast output
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>          
>>>>>
>>>>>>-----Original Message-----
>>>>>>From: Jason Stajich [mailto:jason.stajich at duke.edu]
>>>>>>Sent: Thursday, February 09, 2006 9:13 AM
>>>>>>To: Hubert Prielinger
>>>>>>Cc: Chris Fields; bioperl-l at bioperl.org
>>>>>>Subject: Re: [Bioperl-l] bioperl 1.4 SearchIO doesn't work  
>>>>>>parsing Blast output
>>>>>>
>>>>>>On Feb 8, 2006, at 4:41 PM, Hubert Prielinger wrote:
>>>>>>
>>>>>>
>>>>>>            
>>>>>>
>>>>>>>hi chris,
>>>>>>>thanks, I have upgraded to version 1.5.1 but it isn't still
>>>>>>>
>>>>>>>
>>>>>>>              
>>>>>>>
>>>>>>working,
>>>>>>
>>>>>>
>>>>>>            
>>>>>>
>>>>>>>do you have any ohter idea, the problem I have is that I
>>>>>>>
>>>>>>>
>>>>>>>              
>>>>>>>
>>>>>>have to parse
>>>>>>
>>>>>>
>>>>>>            
>>>>>>
>>>>>>>a lot of textfiles....
>>>>>>>or shall I look for another option to parse those files...
>>>>>>>
>>>>>>>regards
>>>>>>>Hubert
>>>>>>>
>>>>>>>
>>>>>>>              
>>>>>>>
>>>>>>The code from Bioperl 1.5.1 works fine for me for blast
>>>>>>2.2.13 reports but unless you post your blast report we
>>>>>>            
>>>>>>
>>>>can't really
>>>>        
>>>>
>>>>>>determine the problem.
>>>>>>
>>>>>>If you are still getting the same error like this I am not
>>>>>>            
>>>>>>
>>>>convinced
>>>>        
>>>>
>>>>>>you have upgraded to 1.5.1 which includes a fix in the fact
>>>>>>            
>>>>>>
>>>>that NCBI
>>>>        
>>>>
>>>>>>changed the HSP result format to remove the ':' from the
>>>>>>            
>>>>>>
>>>>Query/Sbjct
>>>>        
>>>>
>>>>>>prefixes.  We fixed this as soon as it was apparent sometime in  
>>>>>>September.
>>>>>>
>>>>>>
>>>>>>
>>>>>>            
>>>>>>
>>>>>>>>>MSG: no data for midline Query  1   WWWKWRW  7
>>>>>>>>>STACK Bio::SearchIO::blast::next_result
>>>>>>>>>/usr/lib/perl5/site_perl/5.8.6/Bio/SearchIO/blast.pm:1151
>>>>>>>>>STACK toplevel
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>                  
>>>>>>>>>
>>>>>>/home/Hubert/installed/eclipse/workspace/Database_Search/ 
>>>>>>Blast.pl:21
>>>>>>
>>>>>>If you are just getting no results but also no warnings wrt
>>>>>>            
>>>>>>
>>>>parsing,
>>>>        
>>>>
>>>>>>are you sure your logic is correct?
>>>>>>
>>>>>>If you remove your filters do you see all the HSPS?
>>>>>>
>>>>>>
>>>>>>while (my $result = $search->next_result) {
>>>>>>   print $result->query_name, "\n";
>>>>>>   #iterate over each hit on the query sequence
>>>>>>   while (my $hit = $result->next_hit) {
>>>>>>	print $hit->name, "\n";
>>>>>>       #iterate over each HSP in the hit
>>>>>>       while (my $hsp = $hit->next_hsp) {
>>>>>>	 print $hsp->evalue, " ", $hsp->length('sbjct'), " ", $hsp-
>>>>>>
>>>>>>            
>>>>>>
>>>>>>>hit_string, "\n";	
>>>>>>>
>>>>>>>              
>>>>>>>
>>>>>>      }
>>>>>>  }
>>>>>>}
>>>>>>
>>>>>>
>>>>>>            
>>>>>>
>>>>>I tested some of the BLAST results that Hubert sent Roger
>>>>>          
>>>>>
>>>>and me with a
>>>>        
>>>>
>>>>>similar script to the above.  I removed the file parsing logic  
>>>>>and it
>>>>>
>>>>>          
>>>>>
>>>>seemed
>>>>
>>>>        
>>>>
>>>>>to work just fine.  It may very well be a logic issue or
>>>>>          
>>>>>
>>>>that he hasn't
>>>>        
>>>>
>>>>>installed the latest fix.
>>>>>  It's a funny thing, though.  When I tried using blastcl3 (v.
>>>>>          
>>>>>
>>>>2.2.13),
>>>>        
>>>>
>>>>>even though the returned output was from nr, the top of the  
>>>>>blast output showed that it was v2.2.12:
>>>>>
>>>>>BLASTP 2.2.12 [Aug-07-2005]
>>>>>
>>>>>I double-checked my local version and it's definitely v.2.2.13:
>>>>>-------------------------------------
>>>>>C:\Perl\Scripts>blastcl3 -
>>>>>
>>>>>blastcl3 2.2.13   arguments:...
>>>>>-------------------------------------
>>>>>
>>>>>If you use RemoteBlast using the same settings, the version in  
>>>>>the header looks like this:
>>>>>
>>>>>BLASTP 2.2.13 [Nov-27-2005]
>>>>>
>>>>>I'm wondering if all the blast executables (blast and netblast)  
>>>>>from NCBI have text output like v.2.2.12, while the wwwblast
>>>>>          
>>>>>
>>>>outputs a new
>>>>        
>>>>
>>>>>format (2.2.13).  I'll ask blast-help at NCBI about this.
>>>>>
>>>>>
>>>>>
>>>>>          
>>>>>
>>>>>>To clarify some stuff -
>>>>>>Chris I don't necessarily think the XML is best way forward
>>>>>>            
>>>>>>
>>>>for BLAST
>>>>        
>>>>
>>>>>>reports generated locally, it isn't as detailed as the Text
>>>>>>            
>>>>>>
>>>>format and
>>>>        
>>>>
>>>>>>it is what most people expect to be able to scroll through
>>>>>>            
>>>>>>
>>>>and parse
>>>>        
>>>>
>>>>>>-- it is also harder for the format to change dramatically        
>>>>>>            
>>>>>>
>>>>if you have
>>>>        
>>>>
>>>>>>a static binary on your machine =).  I think for
>>>>>>            
>>>>>>
>>>>remoteblast the XML
>>>>        
>>>>
>>>>>>format should be the way forward but I expect Bioperl to  
>>>>>>maintain support of any plain text BLAST report format that  
>>>>>>people use on a regular basis.
>>>>>>
>>>>>>
>>>>>>
>>>>>>            
>>>>>>
>>>>>Does XML lack some specific info that text output has?
>>>>>          
>>>>>
>>>>Didn't know that.
>>>>I
>>>>
>>>>        
>>>>
>>>>>believe that XML should be default in RemoteBlast since it will  
>>>>>not break, but I agree with you about text output.  I also agree  
>>>>>that it will need somebody to maintain it constantly, much like  
>>>>>RemoteBlast.
>>>>>
>>>>>
>>>>>
>>>>>          
>>>>>
>>>>>>-jason
>>>>>>
>>>>>>
>>>>>>            
>>>>>>
>>>>>>>Chris Fields wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>              
>>>>>>>
>>>>>>>>My guess is you're running into text parsing problems in  
>>>>>>>>Bio::SearchIO::blast.  Upgrade to the latest developer version
>>>>>>>>(1.5.1) or
>>>>>>>>bioperl-live (CVS), then see the bug below.
>>>>>>>>
>>>>>>>>http://bugzilla.bioperl.org/show_bug.cgi?id=1934
>>>>>>>>
>>>>>>>>I think the first problem you ran into is solved in
>>>>>>>>                
>>>>>>>>
>>>>bioperl 1.5.1,
>>>>        
>>>>
>>>>>>>>the last problem (more recent, not related to the first) has  
>>>>>>>>been fixed but hasn't been committed to bioperl-live yet.   
>>>>>>>>The fixed SearchIO::blast is available in the link above, but
>>>>>>>>
>>>>>>>>
>>>>>>>>                
>>>>>>>>
>>>>>>realize it hasn't
>>>>>>
>>>>>>
>>>>>>            
>>>>>>
>>>>>>>>been committed yet and may change.
>>>>>>>>
>>>>>>>>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 Hubert
>>>>        
>>>>
>>>>>>>>>Prielinger
>>>>>>>>>Sent: Wednesday, February 08, 2006 2:52 PM
>>>>>>>>>To: bioperl-l at bioperl.org
>>>>>>>>>Subject: [Bioperl-l] bioperl 1.4 SearchIO doesn't work
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>                  
>>>>>>>>>
>>>>>>parsing Blast
>>>>>>
>>>>>>
>>>>>>            
>>>>>>
>>>>>>>>>output
>>>>>>>>>
>>>>>>>>>Hi,
>>>>>>>>>If I want to parse a Blast Output (Version 2.2.12) with  
>>>>>>>>>Bio::SearchIO, I get the following error message:
>>>>>>>>>
>>>>>>>>>MSG: no data for midline Query  1   WWWKWRW  7
>>>>>>>>>STACK Bio::SearchIO::blast::next_result
>>>>>>>>>/usr/lib/perl5/site_perl/5.8.6/Bio/SearchIO/blast.pm:1151
>>>>>>>>>STACK toplevel
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>                  
>>>>>>>>>
>>>>>>/home/Hubert/installed/eclipse/workspace/Database_Search/ 
>>>>>>Blast.pl:21
>>>>>>
>>>>>>
>>>>>>            
>>>>>>
>>>>>>>>>is that a bug......
>>>>>>>>>
>>>>>>>>>If I want to parse Blast Output (version 2.2.13), I don't  
>>>>>>>>>get anything.....
>>>>>>>>>I'm using bioperl 1.4
>>>>>>>>>
>>>>>>>>>before, I have installed bioperl 1.4, it worked fine
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>                  
>>>>>>>>>
>>>>>>parsing Blast
>>>>>>
>>>>>>
>>>>>>            
>>>>>>
>>>>>>>>>Output (version 2.2.12), but I don't remember which
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>                  
>>>>>>>>>
>>>>>>bioperl version
>>>>>>
>>>>>>
>>>>>>            
>>>>>>
>>>>>>>>>I had installed
>>>>>>>>>
>>>>>>>>>thanks in advance
>>>>>>>>>
>>>>>>>>>Hubert
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>_______________________________________________
>>>>>>>>>Bioperl-l mailing list
>>>>>>>>>Bioperl-l at lists.open-bio.org
>>>>>>>>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>                  
>>>>>>>>>
>>>>>>>>                
>>>>>>>>
>>>>>>>_______________________________________________
>>>>>>>Bioperl-l mailing list
>>>>>>>Bioperl-l at lists.open-bio.org
>>>>>>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>
>>>>>>>
>>>>>>>              
>>>>>>>
>>>>>>--
>>>>>>Jason Stajich
>>>>>>Duke University
>>>>>>http://www.duke.edu/~jes12
>>>>>>
>>>>>>
>>>>>>
>>>>>>            
>>>>>>
>>>>>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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>          
>>>>>
>>>>_______________________________________________
>>>>Bioperl-l mailing list
>>>>Bioperl-l at lists.open-bio.org
>>>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>>
>>>>        
>>>>
>>>
>>>      
>>>
>
>Christopher Fields
>Postdoctoral Researcher
>Lab of Dr. Robert Switzer
>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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