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lib/Bio/DB/SoapEUtilities/FetchAdaptor/seq.pm  view on Meta::CPAN

    }
    return 1;
}
1;

__END__

here\'s an example:

PROTEIN

0  HASH(0x439b8a8)
   'GBSet' => HASH(0x439c010)
      'GBSeq' => HASH(0x43a79c8)
         'GBSeq_accession-version' => 'CAA53922.1'
         'GBSeq_comment' => 'On Nov 8, 1997 this sequence version replaced gi:443947.'
         'GBSeq_create-date' => '18-JAN-1994'
         'GBSeq_definition' => 'sonic hedgehog [Mus musculus]'
         'GBSeq_division' => 'ROD'
         'GBSeq_feature-table' => HASH(0x43abf4c)
            'GBFeature' => HASH(0x43b23b4)
               'GBFeature_intervals' => HASH(0x43b800c)
                  'GBInterval' => HASH(0x43b83fc)
                     'GBInterval_accession' => 'CAA53922.1'
                     'GBInterval_from' => 1
                     'GBInterval_to' => 437
               'GBFeature_key' => 'CDS'
               'GBFeature_location' => '1..437'
               'GBFeature_quals' => HASH(0x43b8378)
                  'GBQualifier' => HASH(0x43baeb0)
                     'GBQualifier_name' => 'db_xref'
                     'GBQualifier_value' => 'UniProtKB/Swiss-Prot:Q62226'
         'GBSeq_length' => 437
         'GBSeq_locus' => 'CAA53922'
         'GBSeq_moltype' => 'AA'
         'GBSeq_organism' => 'Mus musculus'
         'GBSeq_other-seqids' => HASH(0x43ab028)
            'GBSeqid' => 'gi|2597988'
         'GBSeq_primary-accession' => 'CAA53922'
         'GBSeq_references' => HASH(0x43abe80)
            'GBReference' => HASH(0x43af1f8)
               'GBReference_authors' => HASH(0x43af3e4)
                  'GBAuthor' => 'McMahon,A.P.'
               'GBReference_journal' => 'Submitted (03-NOV-1997) A.P. McMahon, Harvard University, 16 Divinity Ave., Cambridge, MA 02138, USA'
               'GBReference_position' => '1..437'
               'GBReference_reference' => 3
               'GBReference_title' => 'Direct Submission'
         'GBSeq_sequence' => 'mllllarcflvilassllvcpglacgpgrgfgkrrhpkkltplaykqfipnvaektlgasgryegkitrnserfkeltpnynpdiifkdeentgadrlmtqrckdklnalaisvmnqwpgvklrvtegwdedghhseeslhyegravdittsdrdrskygmlarlaveagfdwvyyeskahihcsvkaensvaaksggcfpgsatvhleqggtklvkdlr...
         'GBSeq_source' => 'Mus musculus (house mouse)'
         'GBSeq_source-db' => 'embl accession X76290.1'
         'GBSeq_taxonomy' => 'Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; Muridae; Murinae; Mus'
         'GBSeq_topology' => 'linear'
         'GBSeq_update-date' => '04-NOV-1997'

NUCLEOTIDE

0  HASH(0x42c1a44)
   'GBSet' => HASH(0x42dd728)
      'GBSeq' => HASH(0x44bc2c8)
         'GBSeq_accession-version' => 'NR_029721.1'
         'GBSeq_comment' => 'PROVISIONAL REFSEQ: This record is based on preliminary annotation provided by NCBI staff in collaboration with miRBase. The reference sequence was derived from AL645478.15.; ~Summary: microRNAs (miRNAs) are short (20-24 ...
         'GBSeq_create-date' => '29-OCT-2009'
         'GBSeq_definition' => 'Mus musculus microRNA 196a-1 (Mir196a-1), microRNA'
         'GBSeq_division' => 'ROD'
         'GBSeq_feature-table' => HASH(0x4579f0c)
            'GBFeature' => HASH(0x457ab6c)
               'GBFeature_intervals' => HASH(0x457fa20)
                  'GBInterval' => HASH(0x45813d0)
                     'GBInterval_accession' => 'NR_029721.1'
                     'GBInterval_from' => 24
                     'GBInterval_to' => 45
               'GBFeature_key' => 'ncRNA'
               'GBFeature_location' => '24..45'
               'GBFeature_quals' => HASH(0x45813e8)
                  'GBQualifier' => HASH(0x4581a90)
                     'GBQualifier_name' => 'db_xref'
                     'GBQualifier_value' => 'MGI:2676860'
         'GBSeq_length' => 102
         'GBSeq_locus' => 'NR_029721'
         'GBSeq_moltype' => 'ncRNA'
         'GBSeq_organism' => 'Mus musculus'
         'GBSeq_other-seqids' => HASH(0x456bea8)
            'GBSeqid' => 'gi|262205520'
         'GBSeq_primary' => 'REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP~1-102               AL645478.15        79764-79865         '
         'GBSeq_primary-accession' => 'NR_029721'
         'GBSeq_references' => HASH(0x45744ac)
            'GBReference' => HASH(0x457ac20)
               'GBReference_authors' => HASH(0x457f36c)
                  'GBAuthor' => 'Tuschl,T.'
               'GBReference_journal' => 'RNA 9 (2), 175-179 (2003)'
               'GBReference_position' => '1..102'
               'GBReference_pubmed' => 12554859
               'GBReference_reference' => 9
               'GBReference_title' => 'New microRNAs from mouse and human'
         'GBSeq_sequence' => 'tgagccgggactgttgagtgaagtaggtagtttcatgttgttgggcctggctttctgaacacaacgacatcaaaccacctgattcatggcagttactgcttc'
         'GBSeq_source' => 'Mus musculus (house mouse)'
         'GBSeq_strandedness' => 'single'
         'GBSeq_taxonomy' => 'Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; Muridae; Murinae; Mus'
         'GBSeq_topology' => 'linear'
         'GBSeq_update-date' => '06-JAN-2010'