[Bioperl-l] different results with remote-blast skript

[Smithies, Russell]

I'd guess it's a difference in the parameters used.
Interesting that both have the number of letters in the db as "-1,125,070,205", I assume that's a bug  :-)

Stats from your remote_blast:

'stats' => {
             'S1' => '42',
             'S1_bits' => '20.8',
             'lambda' => '0.309',
             'entropy' => '0.345',
             'kappa_gapped' => '0.0410',
             'T' => '11',
             'kappa' => '0.122',
             'X3_bits' => '24.7',
             'X1' => '16',
             'lambda_gapped' => '0.267',
             'X2' => '38',
             'S2' => '74',
             'seqs_better_than_cutoff' => '0',
             'posted_date' => 'Jul 4, 2009  4:41 AM',
             'Hits_to_DB' => '60102303',
             'dbletters' => '-1125070205',
             'A' => '40',
             'num_successful_extensions' => '2004',
             'num_extensions' => '1436892',
             'X1_bits' => '7.1',
             'X3' => '64',
             'entropy_gapped' => '0.140',
             'dbentries' => '9252258',
             'X2_bits' => '14.6',
             'S2_bits' => '33.1'
           }


Stats from a blast done on the NCBI webpage:

  Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF
excluding environmental samples from WGS projects
    Posted date:  Jul 4, 2009  4:41 AM
  Number of letters in database: -1,125,070,205
  Number of sequences in database:  9,252,258

Lambda     K      H
   0.309    0.124    0.340 
Gapped
Lambda     K      H
   0.267   0.0410    0.140 
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 9252258
Number of Hits to DB: 86493230
Number of extensions: 3101413
Number of successful extensions: 9001
Number of sequences better than 100: 65
Number of HSP's better than 100 without gapping: 0
Number of HSP's gapped: 9000
Number of HSP's successfully gapped: 66
Length of query: 150
Length of database: 3169897087
Length adjustment: 113
Effective length of query: 37
Effective length of database: 2124391933
Effective search space: 78602501521
Effective search space used: 78602501521
T: 11
A: 40
X1: 16 (7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (20.8 bits)
S2: 65 (29.6 bits)


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Jonas Schaer
> Sent: Sunday, 28 June 2009 10:15 p.m.
> To: BioPerl List
> Subject: [Bioperl-l] different results with remote-blast skript
> 
> Hi again :)
> please, I only have this little question:
> why do I get different results with my remote::blast perl skript then on the
> ncbi blast homepage?
> I am using blastp, the query is an amino-sequence (different results with any
> sequence, differences not only in number of hits but even in e-values, scores
> etc...), the database is 'nr'.
> PLEASE help me,
> thank you in advance,
> Jonas
> 
> ps: my skript:
> ##############################################################################
> ##
> use Bio::Seq::SeqFactory;
>   use Bio::Tools::Run::RemoteBlast;
>   use strict;
>   my @blast_report;
>   my $prog = 'blastp';
>   my $db   = 'nr';
>   my $e_val= '1e-10';
>   #my $e_val= '10';
>   my @params = ( '-prog' => $prog,
>          '-data' => $db,
>          '-expect' => $e_val,
>          '-readmethod' => 'SearchIO' );
>   my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
>    $Bio::Tools::Run::RemoteBlast::HEADER{'GAPCOSTS'} = '11 1';
>    $Bio::Tools::Run::RemoteBlast::HEADER{'MAX_NUM_SEQ'} = '100';
>  $Bio::Tools::Run::RemoteBlast::HEADER{'EXPECT'} = '10';
> $Bio::Tools::Run::RemoteBlast::HEADER{'COMPOSITION_BASED_STATISTICS'} = '1';
> 
>   my
> $blast_seq='MGSSSVGTYHLLLVLMGAGGEQQAVQAGAEVASTEQVDGSGMAANSRGSTSGSEQPPRDSDLGLLR
> SLLDVAGVDRTALEVKLLALAEAGAEMPPAQDSQATAAGVVATLTSVYRQQVARAWHERDDNAFRQAHQNTAMATGPD
> PDDEYE';
>   #$v is just to turn on and off the messages
>   my $v = 1;
>   my $seqbuilder = Bio::Seq::SeqFactory->new('-type' => 'Bio::PrimarySeq');
>   my $seq = $seqbuilder->create(-seq =>$blast_seq, -display_id =>
> "$blast_seq");
>   my $filename='temp2.out';
>   my $r = $factory->submit_blast($seq);
>   print STDERR "waiting..." if( $v > 0 );
>     while ( my @rids = $factory->each_rid )
>     {
>         foreach my $rid ( @rids )
>         {
>             my $rc = $factory->retrieve_blast($rid);
>             if( !ref($rc) )
>             {
>                 if( $rc < 0 )
>                 {
>                     $factory->remove_rid($rid);
>                 }
>                 print STDERR "." if ( $v > 0 );
>             }
>                 else
>                 {
>                     my $result = $rc->next_result();
>                     $factory->save_output($filename);
>                     $factory->remove_rid($rid);
>                     print "\nQuery Name: ", $result->query_name(), "\n";
>                     while ( my $hit = $result->next_hit )
>                     {
>                         next unless ( $v > 0);
>                         print "\thit name is ", $hit->name, "\n";
>                         while( my $hsp = $hit->next_hsp )
>                         {
>                             print "\t\tscore is ", $hsp->score, "\n";
>                         }
>                     }
>                 }
>         }
> 
> 
>     }
> @blast_report = get_file_data ($filename);
> return @blast_report;
> ##############################################################################
> ####
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