[Bioperl-l] Regarding blast in Bioperl

Mark A. Jensen maj at fortinbras.us
Sat Jan 9 13:05:41 EST 2010


I see it immediately (from making same bug many times) :

 my $factory = Bio::Tools::Run::RemoteBlast->new(@params, -ENTREZ_QUERY =>
- '$organ[ORGN]');
+"$organ[ORGN]");

MAJ

----- Original Message ----- 
From: "Roopa Raghuveer" <rtbio.2009 at gmail.com>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: <bioperl-l at lists.open-bio.org>
Sent: Saturday, January 09, 2010 11:57 AM
Subject: Re: [Bioperl-l] Regarding blast in Bioperl


> Hello all,
> 
> Thanks alot for your reply Mark. It was working for Trypanosoma brucei as
> the organism parameter,but when I tried to use the Organism parameter from
> the user,it was not working i.e., I was unable to get the target sequences.
> Please help me in this regard. My code is
> 
> #!/usr/bin/perl
> 
> #path for extra camel module
> use lib "/srv/www/htdocs/rain/RNAi/";
> use Roopablast;
> 
> 
> use Bio::SearchIO;
> use Bio::Search::Result::BlastResult;
> use Bio::Perl;
> use Bio::Tools::Run::RemoteBlast;
> use Bio::Seq;
> use Bio::SeqIO;
> use Bio::DB::GenBank;
> 
> $serverpath = "/srv/www/htdocs/rain/RNAi";
> $serverurl = "http://141.84.66.66/rain/RNAi";
> $outfile = $serverpath."/rnairesult_".time().".html";
> $nuc = $serverpath."/nuc".time().".txt";
> $debugfile = $serverpath."/debug_".time().".txt";
> $blastdebugfile = $serverpath."/blastdebug_".time().".txt";
> 
> my $outstring ="";
> 
> &parse_form;
> 
> print "Content-type: text/html\n\n";
> print "<HTML>\n";
> print "<head><title>RNAi Result</title>";
> print "<META HTTP-EQUIV=\"Refresh\" CONTENT=\"30;
> URL=$serverurl/rnairesult_".time().".html\"> \n";
> print "</head>\n";
> print "<body>\n";
> print " Your results will appear <a
> href=$serverurl/rnairesult_".time().".html>here</a><br>";
> print " Please be patient, runtime can be up to 5 minutes<br>";
> print " This page will automatically reload in 30 seconds. Roopa";
> print "</BODY>\n";
> print "</HTML>\n";
> 
> defined(my $pid = fork) or die "Can't fork: $!";
> exit if $pid;
> open STDIN, '/dev/null' or die "Can't read /dev/null: $!";
> open STDOUT, '>/dev/null' or die "Can't write to /dev/null: $!";
> open STDERR, '>&STDOUT' or die "Can't dup stdout: $!";
> 
> open(OUTFILE, '>',$outfile);
> 
> print OUTFILE "<HTML>\n
> <head><title>RNAi Result</title>
> <META HTTP-EQUIV=\"Refresh\" CONTENT=\"30;
> URL=$serverurl//rnairesult_".time().".html\"> \n
> <meta http-equiv=\"expires\" content=\"0\">
> </head>\n
> <body>\n
>  Your results will appear <a
> href=$serverurl/rnairesult_".time().".html>here</a><br>
>  Please be patient, runtime can be up to 5 minutes wait wait wait......<br>
> This page will automatically reload in 30 seconds Roopa <br>
> </BODY>\n
> </HTML>\n";
> 
> close(OUTFILE);
> 
> 
> @compseqs = blastcode($in{'Inputseq'},$in{'Organism'});
> 
> $in{'Inputseq'} =~ s/>.*$//m;
> $in{'Inputseq'} =~ s/[^TAGC]//gim;
> $in{'Inputseq'} =~ tr/actg/ACTG/;
> 
> @out = similar($in{'Inputseq'}, \@compseqs, $in{'Windowsize'},
> $in{'Threshold'});
> 
> 
> sub blastcode
> {
> 
> $inpu1= $_[0];
> 
> $organ= $_[1];
> 
> open(NUC,'>',$nuc);
> print NUC $inpu1,"\n";
> close(NUC);
> 
> my $prog = 'blastn';
> my $db   = 'refseq_rna';
> my $e_val= '1e-10';
> my $organism= $organ;
> 
> $gb = new Bio::DB::GenBank;
> 
> my @params = ( '-prog' => $prog,
>         '-data' => $db,
>         '-expect' => $e_val,
>         '-readmethod' => 'SearchIO',
>        '-Organism'   => $organism );
> 
>             open(OUTFILE,'>',$debugfile);
>             print OUTFILE $inpu1;
>              close(OUTFILE);
> 
> 
> my $factory = Bio::Tools::Run::RemoteBlast->new(@params, -ENTREZ_QUERY =>
> '$organ[ORGN]');
> 
> #my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
> 
>  #change a paramter
> 
> #$Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Trypanosoma
> Brucei[ORGN]';
> 
> #change a paramter
> # $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = '$input2[ORGN]';
> 
>  my $v = 1;
>  #$v is just to turn on and off the messages
> 
> my $str = Bio::SeqIO->new('-file' => $nuc , '-format' => 'fasta' ,
> '-organism' => $organ );
> 
> 
> while (my $input = $str->next_seq())
> {
>   #Blast a sequence against a database:
>    #Alternatively, you could  pass in a file with many
>    #sequences rather than loop through sequence one at a time
>    #Remove the loop starting 'while (my $input = $str->next_seq())'
>    #and swap the two lines below for an example of that.
> 
>             #open(OUTFILE,'>',$debugfile);
>              # print OUTFILE $input;
>              #close(OUTFILE);
> 
> 
>   my $r = $factory->submit_blast($input);
> 
>                open(OUTFILE,'>',$debugfile);
>             #   print OUTFILE $r;
>                close(OUTFILE);
> 
>   print STDERR "waiting...." if($v>0);
> 
>  while ( my @rids = $factory->each_rid ) {
>   #   open(OUTFILE,'>',$debugfile);
>    #           print OUTFILE "while entered";
>     #         close(OUTFILE);
>     foreach my $rid ( @rids ) {
> 
>      #         open(OUTFILE,'>',$debugfile);
>       #        print OUTFILE "foreach entered";
>        #      close(OUTFILE);
> 
>        my $rc = $factory->retrieve_blast($rid);
> 
>        if( !ref($rc) )
>        {
>        if( $rc < 0 )
>        {
>        $factory->remove_rid($rid);
>        }
>         open(OUTFILE,'>',$debugfile);
>         #      print OUTFILE "if entered";
>              close(OUTFILE);
>         print STDERR "." if ( $v > 0 );
>         sleep 5;
>        }
>       else {
>          #    open(OUTFILE,'>',$debugfile);
>           #    print OUTFILE "else entered";
>            #  close(OUTFILE);
> 
>          my $result = $rc->next_result();
>         #save the output
>        $blastdebugfile = $serverpath."/blastdebug_".time().".txt";
> 
>          open(BLASTDEBUGFILE,'>',$blastdebugfile);
>          print BLASTDEBUGFILE $result->next_hit();
>          close(BLASTDEBUGFILE);
> 
>        my $filename =
> $serverpath."/blastdata_".time().$result->query_name()."\.out";
> 
>         # open(DEBUGFILE,'>',$debugfile);
>         # open(new,'>',$filename);
>         # @arra=<new>;
>         # print DEBUGFILE @arra;
>         # close(DEBUGFILE);
>         # close(new);
> 
>         $factory->save_output($filename);
>  # open(BLASTDEBUGFILE,'>',$debugfile);
>       # print BLASTDEBUGFILE  "Hello $rid";
>       # close(BLASTDEBUGFILE);
> 
>       $factory->remove_rid($rid);
> 
>       open(BLASTDEBUGFILE,'>',$blastdebugfile);
>       print BLASTDEBUGFILE  $organism;
>        close(BLASTDEBUGFILE);
> 
>    # open(OUTFILE,'>',$outfile);
>    # print OUTFILE "Test2 $result->database_name()";
>    # close(OUTFILE);
> 
> #$hit = $result->next_hit;
> #open(new,'>',$debugfile);
> #print $hit;
> #close(new);
> 
>   while ( my $hit = $result->next_hit ) {
> 
>            next unless ( $v > 0);
> 
>          #     open(OUTFILE,'>',$debugfile);
>           #    print OUTFILE "$hit in while hits";
>            #  close(OUTFILE);
> 
>       my $sequ = $gb->get_Seq_by_version($hit->name);
>           my $dna = $sequ->seq();        # get the sequence as a string
>                  push(@seqs,$dna);
>          }
>        }
>      }
>    }
>  }
> 
>  #open(OUTFILE,'>',$debugfile);
>  #print OUTFILE $seqs[0];
>  #close(OUTFILE);
> 
> return(@seqs);
> 
> }
> 
> Regards,
> Roopa.
> 
> 
> On Fri, Jan 8, 2010 at 4:36 PM, Mark A. Jensen <maj at fortinbras.us> wrote:
> 
>> Hi Roopa--
>>
>> I got your code to work with the following changes:
>>
>> +# the input should be a valid FASTA file...
>> ...
>> open(NUC,'>',$nuc);
>> +print NUC ">seq (need a name line for valid fasta)\n";
>> print NUC $inpu1, "\n";
>> close(NUC);
>> ...
>>
>> +# you can set these header parms in the call itself...
>> - my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
>> + my $factory = Bio::Tools::Run::RemoteBlast->new(@params, -ENTREZ_QUERY =>
>> ''Trypanosoma Brucei[ORGN]');
>>
>>  #change a paramter
>> +# commented this out...
>> +# $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Trypanosoma
>> Brucei[ORGN]';
>>
>> MAJ
>> ----- Original Message ----- From: "Roopa Raghuveer" <rtbio.2009 at gmail.com
>> >
>> To: <bioperl-l at lists.open-bio.org>
>> Sent: Friday, January 08, 2010 10:00 AM
>> Subject: [Bioperl-l] Regarding blast in Bioperl
>>
>>
>>  Hello all,
>>>
>>> I was trying Remote blast using Bioperl. My input data is a Trypanosoma
>>> brucei sequence in Fasta format. When I was trying to submit to BLAST
>>> using
>>> the step
>>> $r=$factory->submit_blast($input)
>>> It was not returning anything which I checked by debugging the code. It is
>>> not blasting my input sequence even though I mentioned all the
>>> parameters.I
>>> would paste the code below.
>>>
>>> Please help me in solving put this problem. It is very urgent.
>>>
>>> Regards
>>> Roopa.
>>>
>>> #!/usr/bin/perl
>>>
>>> #path for extra camel module
>>> use lib "/srv/www/htdocs/rain/RNAi/";
>>> use Roopablast;
>>>
>>>
>>> use Bio::SearchIO;
>>> use Bio::Search::Result::BlastResult;
>>> use Bio::Perl;
>>> use Bio::Tools::Run::RemoteBlast;
>>> use Bio::Seq;
>>> use Bio::SeqIO;
>>> use Bio::DB::GenBank;
>>>
>>> $serverpath = "/srv/www/htdocs/rain/RNAi";
>>> $serverurl = "http://141.84.66.66/rain/RNAi";
>>> $outfile = $serverpath."/rnairesult_".time().".html";
>>> $nuc = $serverpath."/nuc".time().".txt";
>>> $debugfile = $serverpath."/debug_".time().".txt";
>>> $blastdebugfile = $serverpath."/blastdebug_".time().".txt";
>>>
>>> my $outstring ="";
>>>
>>> &parse_form;
>>>
>>> print "Content-type: text/html\n\n";
>>> print "<HTML>\n";
>>> print "<head><title>RNAi Result</title>";
>>> print "<META HTTP-EQUIV=\"Refresh\" CONTENT=\"30;
>>> URL=$serverurl/rnairesult_".time().".html\"> \n";
>>> print "</head>\n";
>>> print "<body>\n";
>>> print " Your results will appear <a
>>> href=$serverurl/rnairesult_".time().".html>here</a><br>";
>>> print " Please be patient, runtime can be up to 5 minutes<br>";
>>> print " This page will automatically reload in 30 seconds. Roopa";
>>> print "</BODY>\n";
>>> print "</HTML>\n";
>>>
>>> defined(my $pid = fork) or die "Can't fork: $!";
>>> exit if $pid;
>>> open STDIN, '/dev/null' or die "Can't read /dev/null: $!";
>>> open STDOUT, '>/dev/null' or die "Can't write to /dev/null: $!";
>>> open STDERR, '>&STDOUT' or die "Can't dup stdout: $!";
>>>
>>>
>>>
>>> open(OUTFILE, '>',$outfile);
>>>
>>> print OUTFILE "<HTML>\n
>>> <head><title>RNAi Result</title>
>>> <META HTTP-EQUIV=\"Refresh\" CONTENT=\"30;
>>> URL=$serverurl//rnairesult_".time().".html\"> \n
>>> <meta http-equiv=\"expires\" content=\"0\">
>>> </head>\n
>>> <body>\n
>>>  Your results will appear <a
>>> href=$serverurl/rnairesult_".time().".html>here</a><br>
>>>  Please be patient, runtime can be up to 5 minutes wait wait
>>> wait......<br>
>>> This page will automatically reload in 30 seconds Roopa <br>
>>> </BODY>\n
>>> </HTML>\n";
>>>
>>> close(OUTFILE);
>>>
>>>
>>> @compseqs = blastcode($in{'Inputseq'});
>>>
>>> $in{'Inputseq'} =~ s/>.*$//m;
>>> $in{'Inputseq'} =~ s/[^TAGC]//gim;
>>> $in{'Inputseq'} =~ tr/actg/ACTG/;
>>>
>>> @out = similar($in{'Inputseq'}, \@compseqs, $in{'Windowsize'},
>>> $in{'Threshold'});
>>>
>>>
>>> sub blastcode
>>> {
>>>
>>> $inpu1= $_[0];
>>>
>>> #$organ= $_[1];
>>>
>>> open(NUC,'>',$nuc);
>>> print NUC $inpu1;
>>> close(NUC);
>>>
>>> my $prog = 'blastn';
>>> my $db   = 'refseq_rna';
>>> my $e_val= '1e-10';
>>> my $organism= 'Trypanosoma Brucei';
>>>
>>> $gb = new Bio::DB::GenBank;
>>>
>>> my @params = ( '-prog' => $prog,
>>>        '-data' => $db,
>>>        '-expect' => $e_val,
>>>        '-readmethod' => 'SearchIO',
>>>        '-Organism'   => $organism );
>>>
>>>           # open(OUTFILE,'>',$debugfile);
>>>            #  print OUTFILE @params;
>>>            # close(OUTFILE);
>>>
>>>
>>> my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
>>>
>>>  #change a paramter
>>>
>>> $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Trypanosoma
>>> Brucei[ORGN]';
>>>
>>> #change a paramter
>>> # $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = '$input2[ORGN]';
>>>
>>>  my $v = 1;
>>>  #$v is just to turn on and off the messages
>>>
>>> my $str = Bio::SeqIO->new('-file' => $nuc , '-format' => 'fasta' ,
>>> '-organism' => 'Trypanosoma Brucei' );
>>>
>>>
>>> while (my $input = $str->next_seq())
>>> {
>>>  #Blast a sequence against a database:
>>>   #Alternatively, you could  pass in a file with many
>>>   #sequences rather than loop through sequence one at a time
>>>   #Remove the loop starting 'while (my $input = $str->next_seq())'
>>>   #and swap the two lines below for an example of that.
>>>
>>>            open(OUTFILE,'>',$debugfile);
>>>              print OUTFILE $input;
>>>             close(OUTFILE);
>>>
>>>
>>>  my $r = $factory->submit_blast($input);    #The program stops here it
>>> does not return any value and it does not enter the While loop,Please help
>>> me in this regard.#
>>>               open(OUTFILE,'>',$debugfile);
>>>               print OUTFILE $r;
>>>               close(OUTFILE);
>>>
>>>
>>>  print STDERR "waiting...." if($v>0);
>>>
>>>  while ( my @rids = $factory->each_rid ) {
>>>     open(OUTFILE,'>',$debugfile);
>>>              print OUTFILE "while entered";
>>>             close(OUTFILE);
>>>    foreach my $rid ( @rids ) {
>>>
>>>              open(OUTFILE,'>',$debugfile);
>>>              print OUTFILE "foreach entered";
>>>             close(OUTFILE);
>>>
>>>       my $rc = $factory->retrieve_blast($rid);
>>>
>>>       if( !ref($rc) )
>>>       {
>>>       if( $rc < 0 )
>>>       {
>>>       $factory->remove_rid($rid);
>>>       }
>>>        open(OUTFILE,'>',$debugfile);
>>>              print OUTFILE "if entered";
>>>             close(OUTFILE);
>>>        print STDERR "." if ( $v > 0 );
>>>        sleep 5;
>>>       }
>>>      else {
>>>             open(OUTFILE,'>',$debugfile);
>>>              print OUTFILE "else entered";
>>>             close(OUTFILE);
>>>
>>>         my $result = $rc->next_result();
>>>        #save the output
>>>       $blastdebugfile = $serverpath."/blastdebug_".time().".txt";
>>>
>>>         open(BLASTDEBUGFILE,'>',$blastdebugfile);
>>>         print BLASTDEBUGFILE $result->next_hit();
>>>         close(BLASTDEBUGFILE);
>>>
>>>       my $filename =
>>> $serverpath."/blastdata_".time().$result->query_name()."\.out";
>>>
>>>        # open(DEBUGFILE,'>',$debugfile);
>>>        # open(new,'>',$filename);
>>>        # @arra=<new>;
>>>        # print DEBUGFILE @arra;
>>>        # close(DEBUGFILE);
>>>        # close(new);
>>>
>>>        $factory->save_output($filename);
>>>
>>>      # open(BLASTDEBUGFILE,'>',$debugfile);
>>>      # print BLASTDEBUGFILE  "Hello $rid";
>>>      # close(BLASTDEBUGFILE);
>>>
>>>      $factory->remove_rid($rid);
>>>
>>>      open(BLASTDEBUGFILE,'>',$blastdebugfile);
>>>      print BLASTDEBUGFILE  $organism;
>>>       close(BLASTDEBUGFILE);
>>>
>>>   # open(OUTFILE,'>',$outfile);
>>>   # print OUTFILE "Test2 $result->database_name()";
>>>   # close(OUTFILE);
>>>
>>> #$hit = $result->next_hit;
>>> #open(new,'>',$debugfile);
>>> #print $hit;
>>> #close(new);
>>>
>>>  while ( my $hit = $result->next_hit ) {
>>>
>>>           next unless ( $v > 0);
>>>
>>>         #     open(OUTFILE,'>',$debugfile);
>>>          #    print OUTFILE "$hit in while hits";
>>>           #  close(OUTFILE);
>>>
>>>      my $sequ = $gb->get_Seq_by_version($hit->name);
>>>          my $dna = $sequ->seq();        # get the sequence as a string
>>>                 push(@seqs,$dna);
>>>         }
>>>       }
>>>     }
>>>   }
>>>  }
>>>
>>>  #open(OUTFILE,'>',$debugfile);
>>>  #print OUTFILE $seqs[0];
>>>  #close(OUTFILE);
>>>
>>> return(@seqs);
>>>
>>> }
>>>
>>> open(OUTFILE, '>',$outfile) || die ;
>>>
>>> print OUTFILE "<HTML>\n
>>> <head><title>RNAi Result</title>
>>> <meta http-equiv=\"expires\" content=\"0\"></head>\n
>>> <body>\n
>>> <p><font face=\"Courier, monospace font set\">
>>> Inputsequence: <br>";
>>>
>>> for ($i=0; $i<length ($in{'Inputseq'}); $i++) {
>>>
>>>   print OUTFILE substr ($in{'Inputseq'}, $i, 1);
>>>
>>>   if ( ($i+1)%10==0){
>>>       print OUTFILE " ";
>>>   }
>>>   if ( ($i+1)%60==0){
>>>       print OUTFILE "<br>\n";
>>>   }
>>> }
>>>
>>>
>>>
>>> print OUTFILE "</font> <p>";
>>>
>>> $z=@compseqs;
>>>
>>> for($k=1;$k<$z;$k++) {
>>>   print OUTFILE "<font face=\"Courier, monospace font set\"><p>Compare
>>> Sequence: <br>";
>>>
>>>   for ($i=0; $i<length ($compseqs[$k]); $i++) {
>>>
>>>       print OUTFILE substr ($compseqs[$k], $i, 1);
>>>
>>>       if ( ($i+1)%10==0){
>>>           print OUTFILE " ";
>>>       }
>>>       if ( ($i+1)%60==0){
>>>           print OUTFILE "<br>\n";
>>>       }
>>>   }
>>>   print OUTFILE "<p></font>";
>>> }
>>>
>>> print OUTFILE "<p>
>>> Window: <br>$in{'Windowsize'}
>>> <p>
>>> <p>
>>> Threshold: <br>$in{'Threshold'}
>>> <p>";
>>> my $j=0;
>>>
>>> for ($i=0; $i<length ($in{'Inputseq'}); $i++) {
>>>
>>>   if ($i<=length ($in{'Inputseq'})-$in{'Windowsize'}){
>>>       if ($out[$i]->{similar}<=$in{'Threshold'}){
>>>           $j=$in{'Windowsize'};
>>>       }
>>>       $height=$out[$i]->{similar}*5;
>>>   }
>>>
>>>   if ($j>0) {
>>>       print OUTFILE "<img src=\"$serverurl/blue.gif\" width=\"1\"
>>> height=\"5\">";
>>>       $outstring .= "<font color=\"green\">".substr ($in{'Inputseq'}, $i,
>>> 1)."</font>";
>>>       $j--;
>>>   }
>>>   else {
>>>       print OUTFILE "<img src=\"$serverurl/red.gif\" width=\"1\"
>>> height=\"5\">";
>>>       $outstring .= "<font color=\"red\">".substr ($in{'Inputseq'}, $i,
>>> 1)."</font>";
>>>   }
>>>
>>>   if ( ($i+1)%10==0){
>>>       $outstring .= " ";
>>>   }
>>>   if ( ($i+1)%60==0){
>>>       $outstring .= "<br>\n";
>>>
>>>   }
>>>   if ( ($i+1)%800==0){
>>>       print OUTFILE "<br><br>\n";
>>>
>>>   }
>>> }
>>>
>>> print OUTFILE "<br><br><font face=\"Courier, monospace font
>>> set\">$outstring</font>";
>>>
>>> #foreach (@out) {
>>> #print OUTFILE "<p>Sequence: $_->{sequence}: $_->{similar} matchs<p>";
>>> #if ($_->{similar}<=$in{'Threshold'}){
>>>
>>> #    }
>>> #}
>>>
>>> print OUTFILE "</BODY>\n</HTML>\n";
>>>
>>> close OUTFILE;
>>>
>>> #nameprint();
>>>
>>> sub parse_form {
>>>   local ($buffer, @pairs, $pair, $name, $value);
>>>   # Read in text
>>>   $ENV{'REQUEST_METHOD'} =~ tr/a-z/A-Z/;
>>>   if ($ENV{'REQUEST_METHOD'} eq "POST")
>>>   {
>>>       read(STDIN, $buffer, $ENV{'CONTENT_LENGTH'});
>>>   }
>>>   else
>>>   {
>>>       $buffer = $ENV{'QUERY_STRING'};
>>>   }
>>>   @pairs = split(/&/, $buffer);
>>>   foreach $pair (@pairs)
>>>   {
>>>       ($name, $value) = split(/=/, $pair);
>>>       $value =~ tr/+/ /;
>>>       $value =~ s/%([a-fA-F0-9][a-fA-F0-9])/pack("C", hex($1))/eg;
>>>       $in{$name} = $value;
>>>   }
>>> }
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
>>
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>


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