Bio-SearchIO-blastxml
view release on metacpan or search on metacpan
lib/Bio/SearchIO/XML/BlastHandler.pm view on Meta::CPAN
'Hsp_pattern-from' => 1,#'patternend',
'Hsp_pattern-to' => 1,#'patternstart',
'Hsp_density' => 1,#'hspdensity',
'Iteration_message' => 1,
'Hit_hsps' => 1,
'BlastOutput_param' => 1,
'Iteration_hits' => 1,
'Statistics' => 1,
'Parameters' => 1,
'BlastOutput' => 1,
'BlastOutput_iterations' => 1,
);
sub start_document{
my ($self) = @_;
$self->{'_lasttype'} = '';
$self->{'_values'} = {};
$self->{'_result'}= [];
}
lib/Bio/SearchIO/XML/PsiBlastHandler.pm view on Meta::CPAN
'Hsp_pattern-from' => 1,#'patternend',
'Hsp_pattern-to' => 1,#'patternstart',
'Hsp_density' => 1,#'hspdensity',
'Iteration_message' => 1,
'Hit_hsps' => 1,
'BlastOutput_param' => 1,
'Iteration_hits' => 1,
'Statistics' => 1,
'Parameters' => 1,
'BlastOutput' => 1,
'BlastOutput_iterations' => 1,
);
sub start_document{
my ($self) = @_;
$self->{'_lasttype'} = '';
$self->{'_values'} = {};
$self->{'_result'}= [];
}
lib/Bio/SearchIO/blastxml.pm view on Meta::CPAN
local $/ = "\n";
local $_;
$self->{'_blastdata'} = '';
my ($sawxmlheader, $okaytoprocess);
my $mode = 'header';
my $tail = << 'XML_END';
</BlastOutput_iterations>
</BlastOutput>
XML_END
# no buffering needed (famous last words...)
my $fh = $self->_fh;
#chop up XML into edible bits for the parser
while( defined( my $line = <$fh>) ) {
next if $line =~ /^\s*$/;
next if $line =~ m{^\s*</BlastOutput_iterations>}xmso || $line =~ m{^</BlastOutput>}xmso;
if( $line =~ m{^RPS-BLAST}i ) {
$self->{'_type'} = 'RPS-BLAST';
next;
} elsif ($line =~ m{^<\?xml\sversion="1.0"}xms) {# <?xml version="1.0"?> & <?xml version="1.0" encoding="UTF-8"?>
delete $self->{'_header'} if exists $self->{'_header'};
$sawxmlheader++;
$mode = 'header';
} elsif ($line =~ m{^\s*<Iteration>}xmso) {
if (!$sawxmlheader) {
if (defined $tfh) {
t/data/ecoli_domains.rps.xml view on Meta::CPAN
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>1e-05</Parameters_expect>
<Parameters_include>0</Parameters_include>
<Parameters_sc-match>0</Parameters_sc-match>
<Parameters_sc-mismatch>0</Parameters_sc-mismatch>
<Parameters_gap-open>11</Parameters_gap-open>
<Parameters_gap-extend>1</Parameters_gap-extend>
<Parameters_filter>F</Parameters_filter>
</Parameters>
</BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_stat>
<Statistics>
<Statistics_db-num>0</Statistics_db-num>
<Statistics_db-len>0</Statistics_db-len>
<Statistics_hsp-len>0</Statistics_hsp-len>
<Statistics_eff-space>4.16497e+11</Statistics_eff-space>
<Statistics_kappa>0.041</Statistics_kappa>
<Statistics_lambda>0.267</Statistics_lambda>
<Statistics_entropy>0.14</Statistics_entropy>
</Statistics>
</Iteration_stat>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd"><BlastOutput>
<BlastOutput_program>blastp</BlastOutput_program>
<BlastOutput_version>blastp 2.1.3 [Apr-1-2001]</BlastOutput_version>
<BlastOutput_reference>~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~p...
<BlastOutput_db>/data_2/jason/db/cdd/cdd/Pfam</BlastOutput_db>
<BlastOutput_query-ID>lcl|QUERY_1</BlastOutput_query-ID>
<BlastOutput_query-def>gi|1786183|gb|AAC73113.1| (AE000111) aspartokinase I, homoserine dehydrogenase I [Escherichia coli]</BlastOutput_query-def>
<BlastOutput_query-len>820</BlastOutput_query-len>
t/data/ecoli_domains.rps.xml view on Meta::CPAN
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>1e-05</Parameters_expect>
<Parameters_include>0</Parameters_include>
<Parameters_sc-match>0</Parameters_sc-match>
<Parameters_sc-mismatch>0</Parameters_sc-mismatch>
<Parameters_gap-open>11</Parameters_gap-open>
<Parameters_gap-extend>1</Parameters_gap-extend>
<Parameters_filter>F</Parameters_filter>
</Parameters>
</BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_hits>
<Hit>
<Hit_num>1</Hit_num>
<Hit_id>gnl|Pfam|pfam00742</Hit_id>
<Hit_def>HomoS_dh, HomoS dehydrogenase</Hit_def>
<Hit_accession>pfam00742</Hit_accession>
<Hit_len>310</Hit_len>
<Hit_hsps>
t/data/ecoli_domains.rps.xml view on Meta::CPAN
<Statistics_db-num>0</Statistics_db-num>
<Statistics_db-len>0</Statistics_db-len>
<Statistics_hsp-len>0</Statistics_hsp-len>
<Statistics_eff-space>3.82682e+07</Statistics_eff-space>
<Statistics_kappa>0.041</Statistics_kappa>
<Statistics_lambda>0.267</Statistics_lambda>
<Statistics_entropy>0.14</Statistics_entropy>
</Statistics>
</Iteration_stat>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd"><BlastOutput>
<BlastOutput_program>blastp</BlastOutput_program>
<BlastOutput_version>blastp 2.1.3 [Apr-1-2001]</BlastOutput_version>
<BlastOutput_reference>~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~p...
<BlastOutput_db>/data_2/jason/db/cdd/cdd/Pfam</BlastOutput_db>
<BlastOutput_query-ID>lcl|QUERY_2</BlastOutput_query-ID>
<BlastOutput_query-def>gi|1786184|gb|AAC73114.1| (AE000111) homoserine kinase [Escherichia coli]</BlastOutput_query-def>
<BlastOutput_query-len>310</BlastOutput_query-len>
t/data/ecoli_domains.rps.xml view on Meta::CPAN
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>1e-05</Parameters_expect>
<Parameters_include>0</Parameters_include>
<Parameters_sc-match>0</Parameters_sc-match>
<Parameters_sc-mismatch>0</Parameters_sc-mismatch>
<Parameters_gap-open>11</Parameters_gap-open>
<Parameters_gap-extend>1</Parameters_gap-extend>
<Parameters_filter>F</Parameters_filter>
</Parameters>
</BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_hits>
<Hit>
<Hit_num>1</Hit_num>
<Hit_id>gnl|Pfam|pfam00288</Hit_id>
<Hit_def>GHMP_kinases, GHMP kinases putative ATP-binding protein</Hit_def>
<Hit_accession>pfam00288</Hit_accession>
<Hit_len>73</Hit_len>
<Hit_hsps>
t/data/ecoli_domains.rps.xml view on Meta::CPAN
<Statistics_db-num>0</Statistics_db-num>
<Statistics_db-len>0</Statistics_db-len>
<Statistics_hsp-len>0</Statistics_hsp-len>
<Statistics_eff-space>3.85928e+07</Statistics_eff-space>
<Statistics_kappa>0.041</Statistics_kappa>
<Statistics_lambda>0.267</Statistics_lambda>
<Statistics_entropy>0.14</Statistics_entropy>
</Statistics>
</Iteration_stat>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd"><BlastOutput>
<BlastOutput_program>blastp</BlastOutput_program>
<BlastOutput_version>blastp 2.1.3 [Apr-1-2001]</BlastOutput_version>
<BlastOutput_reference>~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~p...
<BlastOutput_db>/data_2/jason/db/cdd/cdd/Pfam</BlastOutput_db>
<BlastOutput_query-ID>lcl|QUERY_3</BlastOutput_query-ID>
<BlastOutput_query-def>gi|1786185|gb|AAC73115.1| (AE000111) threonine synthase [Escherichia coli]</BlastOutput_query-def>
<BlastOutput_query-len>428</BlastOutput_query-len>
t/data/ecoli_domains.rps.xml view on Meta::CPAN
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>1e-05</Parameters_expect>
<Parameters_include>0</Parameters_include>
<Parameters_sc-match>0</Parameters_sc-match>
<Parameters_sc-mismatch>0</Parameters_sc-mismatch>
<Parameters_gap-open>11</Parameters_gap-open>
<Parameters_gap-extend>1</Parameters_gap-extend>
<Parameters_filter>F</Parameters_filter>
</Parameters>
</BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_hits>
<Hit>
<Hit_num>1</Hit_num>
<Hit_id>gnl|Pfam|pfam00291</Hit_id>
<Hit_def>PALP, Pyridoxal-phosphate dependent enzyme. Members of this family are all pyridoxal-phosphate dependent enzymes. This family includes: S dehydratase EC:4.2.1.13 P20132, threonine dehydratase EC:4.2.1.16, tryptophan synthase beta c...
<Hit_accession>pfam00291</Hit_accession>
<Hit_len>298</Hit_len>
<Hit_hsps>
t/data/ecoli_domains.rps.xml view on Meta::CPAN
<Statistics_db-num>0</Statistics_db-num>
<Statistics_db-len>0</Statistics_db-len>
<Statistics_hsp-len>0</Statistics_hsp-len>
<Statistics_eff-space>1.52967e+08</Statistics_eff-space>
<Statistics_kappa>0.041</Statistics_kappa>
<Statistics_lambda>0.267</Statistics_lambda>
<Statistics_entropy>0.14</Statistics_entropy>
</Statistics>
</Iteration_stat>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd"><BlastOutput>
<BlastOutput_program>blastp</BlastOutput_program>
<BlastOutput_version>blastp 2.1.3 [Apr-1-2001]</BlastOutput_version>
<BlastOutput_reference>~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~p...
<BlastOutput_db>/data_2/jason/db/cdd/cdd/Pfam</BlastOutput_db>
<BlastOutput_query-ID>lcl|QUERY_4</BlastOutput_query-ID>
<BlastOutput_query-def>gi|1786186|gb|AAC73116.1| (AE000111) orf, hypothetical protein [Escherichia coli]</BlastOutput_query-def>
<BlastOutput_query-len>98</BlastOutput_query-len>
t/data/ecoli_domains.rps.xml view on Meta::CPAN
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>1e-05</Parameters_expect>
<Parameters_include>0</Parameters_include>
<Parameters_sc-match>0</Parameters_sc-match>
<Parameters_sc-mismatch>0</Parameters_sc-mismatch>
<Parameters_gap-open>11</Parameters_gap-open>
<Parameters_gap-extend>1</Parameters_gap-extend>
<Parameters_filter>F</Parameters_filter>
</Parameters>
</BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_stat>
<Statistics>
<Statistics_db-num>0</Statistics_db-num>
<Statistics_db-len>0</Statistics_db-len>
<Statistics_hsp-len>0</Statistics_hsp-len>
<Statistics_eff-space>3.59021e+11</Statistics_eff-space>
<Statistics_kappa>0.041</Statistics_kappa>
<Statistics_lambda>0.267</Statistics_lambda>
<Statistics_entropy>0.14</Statistics_entropy>
</Statistics>
</Iteration_stat>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd"><BlastOutput>
<BlastOutput_program>blastp</BlastOutput_program>
<BlastOutput_version>blastp 2.1.3 [Apr-1-2001]</BlastOutput_version>
<BlastOutput_reference>~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~p...
<BlastOutput_db>/data_2/jason/db/cdd/cdd/Pfam</BlastOutput_db>
<BlastOutput_query-ID>lcl|QUERY_5</BlastOutput_query-ID>
<BlastOutput_query-def>gi|1786187|gb|AAC73117.1| (AE000111) orf, hypothetical protein [Escherichia coli]</BlastOutput_query-def>
<BlastOutput_query-len>258</BlastOutput_query-len>
t/data/ecoli_domains.rps.xml view on Meta::CPAN
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>1e-05</Parameters_expect>
<Parameters_include>0</Parameters_include>
<Parameters_sc-match>0</Parameters_sc-match>
<Parameters_sc-mismatch>0</Parameters_sc-mismatch>
<Parameters_gap-open>11</Parameters_gap-open>
<Parameters_gap-extend>1</Parameters_gap-extend>
<Parameters_filter>F</Parameters_filter>
</Parameters>
</BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_stat>
<Statistics>
<Statistics_db-num>0</Statistics_db-num>
<Statistics_db-len>0</Statistics_db-len>
<Statistics_hsp-len>0</Statistics_hsp-len>
<Statistics_eff-space>3.3722e+11</Statistics_eff-space>
<Statistics_kappa>0.041</Statistics_kappa>
<Statistics_lambda>0.267</Statistics_lambda>
<Statistics_entropy>0.14</Statistics_entropy>
</Statistics>
</Iteration_stat>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd"><BlastOutput>
<BlastOutput_program>blastp</BlastOutput_program>
<BlastOutput_version>blastp 2.1.3 [Apr-1-2001]</BlastOutput_version>
<BlastOutput_reference>~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~p...
<BlastOutput_db>/data_2/jason/db/cdd/cdd/Pfam</BlastOutput_db>
<BlastOutput_query-ID>lcl|QUERY_6</BlastOutput_query-ID>
<BlastOutput_query-def>gi|1786188|gb|AAC73118.1| (AE000111) inner membrane transport protein [Escherichia coli]</BlastOutput_query-def>
<BlastOutput_query-len>476</BlastOutput_query-len>
t/data/ecoli_domains.rps.xml view on Meta::CPAN
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>1e-05</Parameters_expect>
<Parameters_include>0</Parameters_include>
<Parameters_sc-match>0</Parameters_sc-match>
<Parameters_sc-mismatch>0</Parameters_sc-mismatch>
<Parameters_gap-open>11</Parameters_gap-open>
<Parameters_gap-extend>1</Parameters_gap-extend>
<Parameters_filter>F</Parameters_filter>
</Parameters>
</BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_hits>
<Hit>
<Hit_num>1</Hit_num>
<Hit_id>gnl|Pfam|pfam01235</Hit_id>
<Hit_def>Na_Ala_symp, Sodium:alanine symporter family</Hit_def>
<Hit_accession>pfam01235</Hit_accession>
<Hit_len>415</Hit_len>
<Hit_hsps>
t/data/ecoli_domains.rps.xml view on Meta::CPAN
<Statistics_db-num>0</Statistics_db-num>
<Statistics_db-len>0</Statistics_db-len>
<Statistics_hsp-len>0</Statistics_hsp-len>
<Statistics_eff-space>1.95607e+08</Statistics_eff-space>
<Statistics_kappa>0.041</Statistics_kappa>
<Statistics_lambda>0.267</Statistics_lambda>
<Statistics_entropy>0.14</Statistics_entropy>
</Statistics>
</Iteration_stat>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd"><BlastOutput>
<BlastOutput_program>blastp</BlastOutput_program>
<BlastOutput_version>blastp 2.1.3 [Apr-1-2001]</BlastOutput_version>
<BlastOutput_reference>~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~p...
<BlastOutput_db>/data_2/jason/db/cdd/cdd/Pfam</BlastOutput_db>
<BlastOutput_query-ID>lcl|QUERY_7</BlastOutput_query-ID>
<BlastOutput_query-def>gi|1786189|gb|AAC73119.1| (AE000111) transaldolase B [Escherichia coli]</BlastOutput_query-def>
<BlastOutput_query-len>317</BlastOutput_query-len>
t/data/ecoli_domains.rps.xml view on Meta::CPAN
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>1e-05</Parameters_expect>
<Parameters_include>0</Parameters_include>
<Parameters_sc-match>0</Parameters_sc-match>
<Parameters_sc-mismatch>0</Parameters_sc-mismatch>
<Parameters_gap-open>11</Parameters_gap-open>
<Parameters_gap-extend>1</Parameters_gap-extend>
<Parameters_filter>F</Parameters_filter>
</Parameters>
</BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_hits>
<Hit>
<Hit_num>1</Hit_num>
<Hit_id>gnl|Pfam|pfam00923</Hit_id>
<Hit_def>Transaldolase, Transaldolase</Hit_def>
<Hit_accession>pfam00923</Hit_accession>
<Hit_len>282</Hit_len>
<Hit_hsps>
t/data/ecoli_domains.rps.xml view on Meta::CPAN
<Statistics_db-num>0</Statistics_db-num>
<Statistics_db-len>0</Statistics_db-len>
<Statistics_hsp-len>0</Statistics_hsp-len>
<Statistics_eff-space>1.4562e+08</Statistics_eff-space>
<Statistics_kappa>0.041</Statistics_kappa>
<Statistics_lambda>0.267</Statistics_lambda>
<Statistics_entropy>0.14</Statistics_entropy>
</Statistics>
</Iteration_stat>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd"><BlastOutput>
<BlastOutput_program>blastp</BlastOutput_program>
<BlastOutput_version>blastp 2.1.3 [Apr-1-2001]</BlastOutput_version>
<BlastOutput_reference>~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~p...
<BlastOutput_db>/data_2/jason/db/cdd/cdd/Pfam</BlastOutput_db>
<BlastOutput_query-ID>lcl|QUERY_8</BlastOutput_query-ID>
<BlastOutput_query-def>gi|1786190|gb|AAC73120.1| (AE000111) required for the efficient incorporation of molybdate into molybdoproteins [Escherichia coli]</BlastOutput_query-def>
<BlastOutput_query-len>195</BlastOutput_query-len>
t/data/ecoli_domains.rps.xml view on Meta::CPAN
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>1e-05</Parameters_expect>
<Parameters_include>0</Parameters_include>
<Parameters_sc-match>0</Parameters_sc-match>
<Parameters_sc-mismatch>0</Parameters_sc-mismatch>
<Parameters_gap-open>11</Parameters_gap-open>
<Parameters_gap-extend>1</Parameters_gap-extend>
<Parameters_filter>F</Parameters_filter>
</Parameters>
</BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_stat>
<Statistics>
<Statistics_db-num>0</Statistics_db-num>
<Statistics_db-len>0</Statistics_db-len>
<Statistics_hsp-len>0</Statistics_hsp-len>
<Statistics_eff-space>3.35238e+11</Statistics_eff-space>
<Statistics_kappa>0.041</Statistics_kappa>
<Statistics_lambda>0.267</Statistics_lambda>
<Statistics_entropy>0.14</Statistics_entropy>
</Statistics>
</Iteration_stat>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd"><BlastOutput>
<BlastOutput_program>blastp</BlastOutput_program>
<BlastOutput_version>blastp 2.1.3 [Apr-1-2001]</BlastOutput_version>
<BlastOutput_reference>~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~p...
<BlastOutput_db>/data_2/jason/db/cdd/cdd/Pfam</BlastOutput_db>
<BlastOutput_query-ID>lcl|QUERY_9</BlastOutput_query-ID>
<BlastOutput_query-def>gi|1786191|gb|AAC73121.1| (AE000111) orf, hypothetical protein [Escherichia coli]</BlastOutput_query-def>
<BlastOutput_query-len>188</BlastOutput_query-len>
t/data/ecoli_domains.rps.xml view on Meta::CPAN
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>1e-05</Parameters_expect>
<Parameters_include>0</Parameters_include>
<Parameters_sc-match>0</Parameters_sc-match>
<Parameters_sc-mismatch>0</Parameters_sc-mismatch>
<Parameters_gap-open>11</Parameters_gap-open>
<Parameters_gap-extend>1</Parameters_gap-extend>
<Parameters_filter>F</Parameters_filter>
</Parameters>
</BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_hits>
<Hit>
<Hit_num>1</Hit_num>
<Hit_id>gnl|Pfam|pfam01184</Hit_id>
<Hit_def>Grp1_Fun34_YaaH, GPR1/FUN34/yaaH family</Hit_def>
<Hit_accession>pfam01184</Hit_accession>
<Hit_len>210</Hit_len>
<Hit_hsps>
t/data/ecoli_domains.rps.xml view on Meta::CPAN
<Statistics_db-num>0</Statistics_db-num>
<Statistics_db-len>0</Statistics_db-len>
<Statistics_hsp-len>0</Statistics_hsp-len>
<Statistics_eff-space>8.17579e+07</Statistics_eff-space>
<Statistics_kappa>0.041</Statistics_kappa>
<Statistics_lambda>0.267</Statistics_lambda>
<Statistics_entropy>0.14</Statistics_entropy>
</Statistics>
</Iteration_stat>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
t/data/mus.bls.xml view on Meta::CPAN
<BlastOutput_param>
<Parameters>
<Parameters_expect>10</Parameters_expect>
<Parameters_sc-match>1</Parameters_sc-match>
<Parameters_sc-mismatch>-3</Parameters_sc-mismatch>
<Parameters_gap-open>5</Parameters_gap-open>
<Parameters_gap-extend>2</Parameters_gap-extend>
<Parameters_filter>D</Parameters_filter>
</Parameters>
</BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_hits>
<Hit>
<Hit_num>1</Hit_num>
<Hit_id>gnl|BL_ORD_ID|3153</Hit_id>
<Hit_def>NM_001938_up_1000_chr1_93161154_f chr1:93161154-93162153</Hit_def>
<Hit_accession>3153</Hit_accession>
<Hit_len>1000</Hit_len>
<Hit_hsps>
t/data/mus.bls.xml view on Meta::CPAN
<Statistics_db-num>17516</Statistics_db-num>
<Statistics_db-len>17516000</Statistics_db-len>
<Statistics_hsp-len>0</Statistics_hsp-len>
<Statistics_eff-space>1.69255e+10</Statistics_eff-space>
<Statistics_kappa>0.710605</Statistics_kappa>
<Statistics_lambda>1.37407</Statistics_lambda>
<Statistics_entropy>1.30725</Statistics_entropy>
</Statistics>
</Iteration_stat>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
t/data/newblast.xml view on Meta::CPAN
<BlastOutput_query-def>dihydroorotase [Pseudomonas aeruginosa PAO1]</BlastOutput_query-def>
<BlastOutput_query-len>445</BlastOutput_query-len>
<BlastOutput_param>
<Parameters>
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>10</Parameters_expect>
<Parameters_gap-open>11</Parameters_gap-open>
<Parameters_gap-extend>1</Parameters_gap-extend>
</Parameters>
</BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_query-ID>gi|15600734|ref|NP_254228.1|</Iteration_query-ID>
<Iteration_query-def>dihydroorotase [Pseudomonas aeruginosa PAO1]</Iteration_query-def>
<Iteration_query-len>445</Iteration_query-len>
<Iteration_hits>
<Hit>
<Hit_num>1</Hit_num>
<Hit_id>gi|15600734|ref|NP_254228.1|</Hit_id>
<Hit_def>dihydroorotase [Pseudomonas aeruginosa PAO1] >gi|107104643|ref|ZP_01368561.1| hypothetical protein PaerPA_01005722 [Pseudomonas aeruginosa PACS2] >gi|9951880|gb|AAG08926.1|AE004966_8 dihydroorotase [Pseudomonas aeruginosa PAO...
t/data/newblast.xml view on Meta::CPAN
<Statistics_db-num>4299737</Statistics_db-num>
<Statistics_db-len>1479795817</Statistics_db-len>
<Statistics_hsp-len>0</Statistics_hsp-len>
<Statistics_eff-space>0</Statistics_eff-space>
<Statistics_kappa>0.041</Statistics_kappa>
<Statistics_lambda>0.267</Statistics_lambda>
<Statistics_entropy>0.14</Statistics_entropy>
</Statistics>
</Iteration_stat>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
t/data/plague_yeast.bls.xml view on Meta::CPAN
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>0.1</Parameters_expect>
<Parameters_include>0</Parameters_include>
<Parameters_sc-match>0</Parameters_sc-match>
<Parameters_sc-mismatch>0</Parameters_sc-mismatch>
<Parameters_gap-open>11</Parameters_gap-open>
<Parameters_gap-extend>1</Parameters_gap-extend>
<Parameters_filter>S</Parameters_filter>
</Parameters>
</BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_stat>
<Statistics>
<Statistics_db-num>6298</Statistics_db-num>
<Statistics_db-len>2974038</Statistics_db-len>
<Statistics_hsp-len>0</Statistics_hsp-len>
<Statistics_eff-space>8.07438e+08</Statistics_eff-space>
<Statistics_kappa>0.041</Statistics_kappa>
<Statistics_lambda>0.267</Statistics_lambda>
<Statistics_entropy>0.14</Statistics_entropy>
</Statistics>
</Iteration_stat>
<Iteration_message>No hits found</Iteration_message>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd"><BlastOutput>
<BlastOutput_program>blastp</BlastOutput_program>
<BlastOutput_version>blastp 2.1.3 [Apr-11-2001]</BlastOutput_version>
<BlastOutput_reference>~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~p...
<BlastOutput_db>yeast.aa</BlastOutput_db>
<BlastOutput_query-ID>lcl|QUERY</BlastOutput_query-ID>
<BlastOutput_query-def>gi|5763812|emb|CAB53165.1| putative ATP-binding protein [Yersinia pestis]</BlastOutput_query-def>
<BlastOutput_query-len>260</BlastOutput_query-len>
t/data/plague_yeast.bls.xml view on Meta::CPAN
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>0.1</Parameters_expect>
<Parameters_include>0</Parameters_include>
<Parameters_sc-match>0</Parameters_sc-match>
<Parameters_sc-mismatch>0</Parameters_sc-mismatch>
<Parameters_gap-open>11</Parameters_gap-open>
<Parameters_gap-extend>1</Parameters_gap-extend>
<Parameters_filter>S</Parameters_filter>
</Parameters>
</BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_stat>
<Statistics>
<Statistics_db-num>6298</Statistics_db-num>
<Statistics_db-len>2974038</Statistics_db-len>
<Statistics_hsp-len>0</Statistics_hsp-len>
<Statistics_eff-space>5.66408e+08</Statistics_eff-space>
<Statistics_kappa>0.041</Statistics_kappa>
<Statistics_lambda>0.267</Statistics_lambda>
<Statistics_entropy>0.14</Statistics_entropy>
</Statistics>
</Iteration_stat>
<Iteration_message>No hits found</Iteration_message>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd"><BlastOutput>
<BlastOutput_program>blastp</BlastOutput_program>
<BlastOutput_version>blastp 2.1.3 [Apr-11-2001]</BlastOutput_version>
<BlastOutput_reference>~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~p...
<BlastOutput_db>yeast.aa</BlastOutput_db>
<BlastOutput_query-ID>lcl|QUERY</BlastOutput_query-ID>
<BlastOutput_query-def>gi|5763813|emb|CAB53166.1| putative replication regulatory protein [Yersinia pestis]</BlastOutput_query-def>
<BlastOutput_query-len>64</BlastOutput_query-len>
t/data/plague_yeast.bls.xml view on Meta::CPAN
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>0.1</Parameters_expect>
<Parameters_include>0</Parameters_include>
<Parameters_sc-match>0</Parameters_sc-match>
<Parameters_sc-mismatch>0</Parameters_sc-mismatch>
<Parameters_gap-open>11</Parameters_gap-open>
<Parameters_gap-extend>1</Parameters_gap-extend>
<Parameters_filter>S</Parameters_filter>
</Parameters>
</BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_stat>
<Statistics>
<Statistics_db-num>6298</Statistics_db-num>
<Statistics_db-len>2974038</Statistics_db-len>
<Statistics_hsp-len>0</Statistics_hsp-len>
<Statistics_eff-space>6.53308e+07</Statistics_eff-space>
<Statistics_kappa>0.041</Statistics_kappa>
<Statistics_lambda>0.267</Statistics_lambda>
<Statistics_entropy>0.14</Statistics_entropy>
</Statistics>
</Iteration_stat>
<Iteration_message>No hits found</Iteration_message>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd"><BlastOutput>
<BlastOutput_program>blastp</BlastOutput_program>
<BlastOutput_version>blastp 2.1.3 [Apr-11-2001]</BlastOutput_version>
<BlastOutput_reference>~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~p...
<BlastOutput_db>yeast.aa</BlastOutput_db>
<BlastOutput_query-ID>lcl|QUERY</BlastOutput_query-ID>
<BlastOutput_query-def>gi|5763814|emb|CAB53167.1| pesticin immunity protein [Yersinia pestis]</BlastOutput_query-def>
<BlastOutput_query-len>141</BlastOutput_query-len>
t/data/plague_yeast.bls.xml view on Meta::CPAN
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>0.1</Parameters_expect>
<Parameters_include>0</Parameters_include>
<Parameters_sc-match>0</Parameters_sc-match>
<Parameters_sc-mismatch>0</Parameters_sc-mismatch>
<Parameters_gap-open>11</Parameters_gap-open>
<Parameters_gap-extend>1</Parameters_gap-extend>
<Parameters_filter>S</Parameters_filter>
</Parameters>
</BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_stat>
<Statistics>
<Statistics_db-num>6298</Statistics_db-num>
<Statistics_db-len>2974038</Statistics_db-len>
<Statistics_hsp-len>0</Statistics_hsp-len>
<Statistics_eff-space>2.68243e+08</Statistics_eff-space>
<Statistics_kappa>0.041</Statistics_kappa>
<Statistics_lambda>0.267</Statistics_lambda>
<Statistics_entropy>0.14</Statistics_entropy>
</Statistics>
</Iteration_stat>
<Iteration_message>No hits found</Iteration_message>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd"><BlastOutput>
<BlastOutput_program>blastp</BlastOutput_program>
<BlastOutput_version>blastp 2.1.3 [Apr-11-2001]</BlastOutput_version>
<BlastOutput_reference>~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~p...
<BlastOutput_db>yeast.aa</BlastOutput_db>
<BlastOutput_query-ID>lcl|QUERY</BlastOutput_query-ID>
<BlastOutput_query-def>gi|5763815|emb|CAB53168.1| pesticin [Yersinia pestis]</BlastOutput_query-def>
<BlastOutput_query-len>357</BlastOutput_query-len>
t/data/plague_yeast.bls.xml view on Meta::CPAN
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>0.1</Parameters_expect>
<Parameters_include>0</Parameters_include>
<Parameters_sc-match>0</Parameters_sc-match>
<Parameters_sc-mismatch>0</Parameters_sc-mismatch>
<Parameters_gap-open>11</Parameters_gap-open>
<Parameters_gap-extend>1</Parameters_gap-extend>
<Parameters_filter>S</Parameters_filter>
</Parameters>
</BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_hits>
<Hit>
<Hit_num>1</Hit_num>
<Hit_id>gi|6320063|ref|NP_010143.1|</Hit_id>
<Hit_def>glucose permease; Rgt2p</Hit_def>
<Hit_accession>NP_010143</Hit_accession>
<Hit_len>763</Hit_len>
<Hit_hsps>
t/data/plague_yeast.bls.xml view on Meta::CPAN
<Statistics_db-num>6298</Statistics_db-num>
<Statistics_db-len>2974038</Statistics_db-len>
<Statistics_hsp-len>0</Statistics_hsp-len>
<Statistics_eff-space>8.3019e+08</Statistics_eff-space>
<Statistics_kappa>0.041</Statistics_kappa>
<Statistics_lambda>0.267</Statistics_lambda>
<Statistics_entropy>0.14</Statistics_entropy>
</Statistics>
</Iteration_stat>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd"><BlastOutput>
<BlastOutput_program>blastp</BlastOutput_program>
<BlastOutput_version>blastp 2.1.3 [Apr-11-2001]</BlastOutput_version>
<BlastOutput_reference>~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~p...
<BlastOutput_db>yeast.aa</BlastOutput_db>
<BlastOutput_query-ID>lcl|QUERY</BlastOutput_query-ID>
<BlastOutput_query-def>gi|5763816|emb|CAB53169.1| hypothetical protein [Yersinia pestis]</BlastOutput_query-def>
<BlastOutput_query-len>138</BlastOutput_query-len>
t/data/plague_yeast.bls.xml view on Meta::CPAN
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>0.1</Parameters_expect>
<Parameters_include>0</Parameters_include>
<Parameters_sc-match>0</Parameters_sc-match>
<Parameters_sc-mismatch>0</Parameters_sc-mismatch>
<Parameters_gap-open>11</Parameters_gap-open>
<Parameters_gap-extend>1</Parameters_gap-extend>
<Parameters_filter>S</Parameters_filter>
</Parameters>
</BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_stat>
<Statistics>
<Statistics_db-num>6298</Statistics_db-num>
<Statistics_db-len>2974038</Statistics_db-len>
<Statistics_hsp-len>0</Statistics_hsp-len>
<Statistics_eff-space>2.46958e+08</Statistics_eff-space>
<Statistics_kappa>0.041</Statistics_kappa>
<Statistics_lambda>0.267</Statistics_lambda>
<Statistics_entropy>0.14</Statistics_entropy>
</Statistics>
</Iteration_stat>
<Iteration_message>No hits found</Iteration_message>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd"><BlastOutput>
<BlastOutput_program>blastp</BlastOutput_program>
<BlastOutput_version>blastp 2.1.3 [Apr-11-2001]</BlastOutput_version>
<BlastOutput_reference>~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~p...
<BlastOutput_db>yeast.aa</BlastOutput_db>
<BlastOutput_query-ID>lcl|QUERY</BlastOutput_query-ID>
<BlastOutput_query-def>gi|5763817|emb|CAB53170.1| coagulase/fibrinolysin precursor [Yersinia pestis]</BlastOutput_query-def>
<BlastOutput_query-len>312</BlastOutput_query-len>
t/data/plague_yeast.bls.xml view on Meta::CPAN
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>0.1</Parameters_expect>
<Parameters_include>0</Parameters_include>
<Parameters_sc-match>0</Parameters_sc-match>
<Parameters_sc-mismatch>0</Parameters_sc-mismatch>
<Parameters_gap-open>11</Parameters_gap-open>
<Parameters_gap-extend>1</Parameters_gap-extend>
<Parameters_filter>S</Parameters_filter>
</Parameters>
</BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_stat>
<Statistics>
<Statistics_db-num>6298</Statistics_db-num>
<Statistics_db-len>2974038</Statistics_db-len>
<Statistics_hsp-len>0</Statistics_hsp-len>
<Statistics_eff-space>7.18398e+08</Statistics_eff-space>
<Statistics_kappa>0.041</Statistics_kappa>
<Statistics_lambda>0.267</Statistics_lambda>
<Statistics_entropy>0.14</Statistics_entropy>
</Statistics>
</Iteration_stat>
<Iteration_message>No hits found</Iteration_message>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd"><BlastOutput>
<BlastOutput_program>blastp</BlastOutput_program>
<BlastOutput_version>blastp 2.1.3 [Apr-11-2001]</BlastOutput_version>
<BlastOutput_reference>~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~p...
<BlastOutput_db>yeast.aa</BlastOutput_db>
<BlastOutput_query-ID>lcl|QUERY</BlastOutput_query-ID>
<BlastOutput_query-def>gi|5763818|emb|CAB53171.1| putative transcriptional regulator [Yersinia pestis]</BlastOutput_query-def>
<BlastOutput_query-len>99</BlastOutput_query-len>
t/data/plague_yeast.bls.xml view on Meta::CPAN
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>0.1</Parameters_expect>
<Parameters_include>0</Parameters_include>
<Parameters_sc-match>0</Parameters_sc-match>
<Parameters_sc-mismatch>0</Parameters_sc-mismatch>
<Parameters_gap-open>11</Parameters_gap-open>
<Parameters_gap-extend>1</Parameters_gap-extend>
<Parameters_filter>S</Parameters_filter>
</Parameters>
</BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_stat>
<Statistics>
<Statistics_db-num>6298</Statistics_db-num>
<Statistics_db-len>2974038</Statistics_db-len>
<Statistics_hsp-len>0</Statistics_hsp-len>
<Statistics_eff-space>1.39258e+08</Statistics_eff-space>
<Statistics_kappa>0.041</Statistics_kappa>
<Statistics_lambda>0.267</Statistics_lambda>
<Statistics_entropy>0.14</Statistics_entropy>
</Statistics>
</Iteration_stat>
<Iteration_message>No hits found</Iteration_message>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd"><BlastOutput>
<BlastOutput_program>blastp</BlastOutput_program>
<BlastOutput_version>blastp 2.1.3 [Apr-11-2001]</BlastOutput_version>
<BlastOutput_reference>~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~p...
<BlastOutput_db>yeast.aa</BlastOutput_db>
<BlastOutput_query-ID>lcl|QUERY</BlastOutput_query-ID>
<BlastOutput_query-def>gi|5763819|emb|CAB53172.1| hypothetical protein [Yersinia pestis]</BlastOutput_query-def>
<BlastOutput_query-len>115</BlastOutput_query-len>
t/data/plague_yeast.bls.xml view on Meta::CPAN
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>0.1</Parameters_expect>
<Parameters_include>0</Parameters_include>
<Parameters_sc-match>0</Parameters_sc-match>
<Parameters_sc-mismatch>0</Parameters_sc-mismatch>
<Parameters_gap-open>11</Parameters_gap-open>
<Parameters_gap-extend>1</Parameters_gap-extend>
<Parameters_filter>S</Parameters_filter>
</Parameters>
</BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_stat>
<Statistics>
<Statistics_db-num>6298</Statistics_db-num>
<Statistics_db-len>2974038</Statistics_db-len>
<Statistics_hsp-len>0</Statistics_hsp-len>
<Statistics_eff-space>2.00971e+08</Statistics_eff-space>
<Statistics_kappa>0.041</Statistics_kappa>
<Statistics_lambda>0.267</Statistics_lambda>
<Statistics_entropy>0.14</Statistics_entropy>
</Statistics>
</Iteration_stat>
<Iteration_message>No hits found</Iteration_message>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
t/data/psiblast.xml view on Meta::CPAN
<BlastOutput_param>
<Parameters>
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>10</Parameters_expect>
<Parameters_include>0.002</Parameters_include>
<Parameters_gap-open>11</Parameters_gap-open>
<Parameters_gap-extend>1</Parameters_gap-extend>
<Parameters_filter>F</Parameters_filter>
</Parameters>
</BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_hits>
<Hit>
<Hit_num>1</Hit_num>
<Hit_id>gi|16411294|emb|CAC99918.1|</Hit_id>
<Hit_def>pyrR [Listeria monocytogenes]</Hit_def>
<Hit_accession>CAC99918</Hit_accession>
<Hit_len>183</Hit_len>
<Hit_hsps>
t/data/psiblast.xml view on Meta::CPAN
<Statistics_db-len>870878</Statistics_db-len>
<Statistics_hsp-len>75</Statistics_hsp-len>
<Statistics_eff-space>6.44279e+07</Statistics_eff-space>
<Statistics_kappa>0.0475563</Statistics_kappa>
<Statistics_lambda>0.267</Statistics_lambda>
<Statistics_entropy>0.14</Statistics_entropy>
</Statistics>
</Iteration_stat>
<Iteration_message>CONVERGED</Iteration_message>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
<BlastOutput>
<BlastOutput_program>blastp</BlastOutput_program>
<BlastOutput_version>blastp 2.2.16 [Mar-25-2007]</BlastOutput_version>
<BlastOutput_reference>~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~p...
<BlastOutput_db>AL591824.faa</BlastOutput_db>
<BlastOutput_query-ID>lcl|QUERY</BlastOutput_query-ID>
<BlastOutput_query-def>gi|154350371|gb|ABS72450.1| DnaN [Bacillus amyloliquefaciens FZB42]</BlastOutput_query-def>
t/data/psiblast.xml view on Meta::CPAN
<BlastOutput_param>
<Parameters>
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>10</Parameters_expect>
<Parameters_include>0.002</Parameters_include>
<Parameters_gap-open>11</Parameters_gap-open>
<Parameters_gap-extend>1</Parameters_gap-extend>
<Parameters_filter>F</Parameters_filter>
</Parameters>
</BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_hits>
<Hit>
<Hit_num>1</Hit_num>
<Hit_id>gi|16409361|emb|CAC98217.1|</Hit_id>
<Hit_def>DNA polymerase III, beta chain [Listeria monocytogenes]</Hit_def>
<Hit_accession>CAC98217</Hit_accession>
<Hit_len>381</Hit_len>
<Hit_hsps>
t/data/psiblast.xml view on Meta::CPAN
<Statistics_db-len>870878</Statistics_db-len>
<Statistics_hsp-len>82</Statistics_hsp-len>
<Statistics_eff-space>1.88702e+08</Statistics_eff-space>
<Statistics_kappa>0.0450367</Statistics_kappa>
<Statistics_lambda>0.267</Statistics_lambda>
<Statistics_entropy>0.14</Statistics_entropy>
</Statistics>
</Iteration_stat>
<Iteration_message>CONVERGED</Iteration_message>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
( run in 2.466 seconds using v1.01-cache-2.11-cpan-96521ef73a4 )