BioPerl

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Bio/Seq/BaseSeqProcessor.pm  view on Meta::CPAN

=cut

sub object_factory{
    return shift->sequence_factory(@_);
}

=head2 close

 Title   : close
 Usage   :
 Function: Closes the stream. We override this here in order to cascade
           to the source stream.
 Example :
 Returns : 
 Args    : none


=cut

sub close{
    my $self = shift;

t/data/entrezgene.dat  view on Meta::CPAN

          source {
            {
              src {
                db "05010" ,
                tag
                  str "05010" } ,
              anchor "05010" ,
              url "http://www.genome.jp/dbget-bin/show_pathway?hsa05010+2" } } } ,
        {
          type comment ,
          text "KEGG pathway: Coagulation cascade" ,
          version 0 ,
          source {
            {
              src {
                db "04610" ,
                tag
                  str "04610" } ,
              anchor "04610" ,
              url "http://www.genome.jp/dbget-bin/show_pathway?hsa04610+2" } } } ,
        {
          type comment ,
          text "KEGG pathway: Complement and coagulation cascades" ,
          version 0 ,
          source {
            {
              src {
                db "04610" ,
                tag
                  str "04610" } ,
              anchor "04610" ,
              url "http://www.genome.jp/dbget-bin/show_pathway?hsa04610+2" } } } ,
        {

t/data/interpro.xml  view on Meta::CPAN

    <taxon_data name="Plastid Group" proteins_count="11"/>
    <taxon_data name="Other Eukaryotes" proteins_count="4"/>
  </taxonomy_distribution>
  <sec_list>
    <sec_ac acc="IPR001713"/>
  </sec_list>
</interpro>
<interpro id="IPR000011" protein_count="359" short_name="UBQ-activ_enz_E1-like" type="Region">
  <name>Ubiquitin-activating enzyme, E1-like</name>
  <abstract>
<p>The post-translational attachment of ubiquitin (<db_xref db="INTERPRO" dbkey="IPR000626"/>) to proteins (ubiquitinylation) alters the function, location or trafficking of a protein, or targets it to the 26S proteasome for degradation [<cite idref=...
</abstract>
  <class_list>
    <classification id="GO:0006464" class_type="GO">
      <category>Biological Process</category>
      <description>protein modification process</description>
    </classification>
    <classification id="GO:0008641" class_type="GO">
      <category>Molecular Function</category>
      <description>small protein activating enzyme activity</description>
    </classification>

t/data/interpro_relationship.xml  view on Meta::CPAN

    <taxon_data name="Plastid Group" proteins_count="11"/>
    <taxon_data name="Other Eukaryotes" proteins_count="4"/>
  </taxonomy_distribution>
  <sec_list>
    <sec_ac acc="IPR001713"/>
  </sec_list>
</interpro>
<interpro id="IPR000011" protein_count="359" short_name="UBQ-activ_enz_E1-like" type="Region">
  <name>Ubiquitin-activating enzyme, E1-like</name>
  <abstract>
<p>The post-translational attachment of ubiquitin (<db_xref db="INTERPRO" dbkey="IPR000626"/>) to proteins (ubiquitinylation) alters the function, location or trafficking of a protein, or targets it to the 26S proteasome for degradation [<cite idref=...
</abstract>
  <class_list>
    <classification id="GO:0006464" class_type="GO">
      <category>Biological Process</category>
      <description>protein modification process</description>
    </classification>
    <classification id="GO:0008641" class_type="GO">
      <category>Molecular Function</category>
      <description>small protein activating enzyme activity</description>
    </classification>

t/data/interpro_relationship.xml  view on Meta::CPAN

    <taxon_data name="Arthropoda" proteins_count="1"/>
    <taxon_data name="Metazoa" proteins_count="3"/>
    <taxon_data name="Plastid Group" proteins_count="1"/>
  </taxonomy_distribution>
</interpro>
<interpro id="IPR000038" protein_count="1164" short_name="Cell_Div_GTP-bd" type="Family">
  <name>Cell division/GTP binding protein</name>
  <abstract>
<p>Septins constitute a eukaryotic family of guanine nucleotide-binding proteins, most of which polymerise to form filaments [<cite idref="PUB00021050"/>]. Members of the family were first identified by genetic screening for <taxon tax_id="4932">Sacc...
<p>Septins are approximately 40-50 kDa in molecular mass, and typically comprise a conserved central core domain (more than 35% sequence identity between mammalian and yeast homologues) flanked by more divergent N- and C-termini. Most septins possess...
<p>A number of septin interaction partners have been identified in yeast, many of which are components of the budding site selection machinery, kinase cascades or of the ubiquitination pathway. It has been proposed that septins may act as a scaffold ...
<p>This entry represents a variety of septins and homologous sequences involved in the cell division process.</p>
</abstract>
  <class_list>
    <classification id="GO:0005525" class_type="GO">
      <category>Molecular Function</category>
      <description>GTP binding</description>
    </classification>
    <classification id="GO:0007049" class_type="GO">
      <category>Biological Process</category>
      <description>cell cycle</description>

t/data/sv40_small.xml  view on Meta::CPAN

           </names>
           <xref>
             <primaryRef db="uniprotkb" id="O14508" secondary="socs2_human" version="SP_49"/>
             <secondaryRef db="go" id="GO:0005737" secondary="C:cytoplasm"/>
             <secondaryRef db="go" id="GO:0005131" secondary="F:growth hormone receptor bind"/>
             <secondaryRef db="go" id="GO:0005159" secondary="F:insulin-like growth factor r"/>
             <secondaryRef db="go" id="GO:0008269" secondary="F:JAK pathway signal transduct"/>
             <secondaryRef db="go" id="GO:0005148" secondary="F:prolactin receptor binding"/>
             <secondaryRef db="go" id="GO:0005070" secondary="F:SH3/SH2 adaptor activity"/>
             <secondaryRef db="go" id="GO:0006916" secondary="P:anti-apoptosis"/>
             <secondaryRef db="go" id="GO:0007259" secondary="P:JAK-STAT cascade"/>
             <secondaryRef db="go" id="GO:0045666" secondary="P:positive regulation of neuro"/>
             <secondaryRef db="go" id="GO:0040014" secondary="P:regulation of body size"/>
             <secondaryRef db="go" id="GO:0001558" secondary="P:regulation of cell growth"/>
             <secondaryRef db="go" id="GO:0009966" secondary="P:regulation of signal transdu"/>
             <secondaryRef db="interpro" id="IPR000980" secondary="SH2"/>
             <secondaryRef db="interpro" id="IPR001496" secondary="SOCS_C"/>
             <secondaryRef db="uniprotkb" id="O14542" secondary="socs2_human" version="SP_49"/>
             <secondaryRef db="uniprotkb" id="O95102" secondary="socs2_human" version="SP_49"/>
             <secondaryRef db="uniprotkb" id="Q9UKS5" secondary="socs2_human" version="SP_49"/>
             <secondaryRef db="go" id="GO:0005515" secondary="F:protein binding"/>