XrefMapper rattus_norvegicus
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Package variables
No package variables defined.
Included modules
XrefMapper::BasicMapper
Inherit
XrefMapper::BasicMapper
Synopsis
No synopsis!
Description
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Methods
gene_description_filter_regexps
No description
Code
get_set_lists
No description
Code
transcript_display_xref_sources
No description
Code
Methods description
None available.
Methods code
gene_description_filter_regexpsdescriptionprevnextTop
sub gene_description_filter_regexps {
  return ('^\(CLONE REM\d+\) ORF\( FRAGMENT\)\.*',
	  '^ORF\s*\d+\s+PROTEIN\.*',
	  '\(?[0-9A-Z]{10}RIK PROTEIN\)?[\. ]',
	  'RIKEN CDNA [0-9A-Z]{10}[\. ;]',
	  '.*RIKEN FULL-LENGTH ENRICHED LIBRARY.*PRODUCT:',
	  '.*RIKEN FULL-LENGTH ENRICHED LIBRARY.*',
	  '\(*HYPOTHETICAL\s+.*',
	  '^UNKNOWN\s+.*',
	  'CDNA SEQUENCE\s?,? [A-Z]+\d+[\. ;]',
	  'CLONE MGC:\d+[\. ;]',
	  'MGC:\s*\d+[\. ;]',
	  'HYPOTHETICAL PROTEIN,',
	  'HYPOTHETICAL PROTEIN\S +[\.;]',
	  'DNA SEGMENT, CHR.*',
	  'PROTEIN\S + HOMOLOG\.?',
	  '^SIMILAR TO GENE.*',
	  'SIMILAR TO PUTATIVE[\. ]',
	  '^SIMILAR TO HYPOTHETICAL.*',
	  'SIMILAR TO (KIAA|LOC|RIKEN).*',
	  'SIMILAR TO GENBANK ACCESSION NUMBER\s+\S+',
	  'SIMILAR TO\s+$',
          'EXPRESSED SEQUENCE [A-Z]+\d+[\. ;]',
          'EST [A-Z]+\d+[\. ;]',
          '^\s*\(FRAGMENT\)\.?\s*$',
	  '^\s*\(?GENE\)?\.?;?\s*$',
          '\s*\(?GENE\)?\.?;?',
          '\s*\(?PRECURSOR\)?\.?;?',
          '^\s*\(\s*\)\s*$',
	  '^\s*\(\d*\)\s*[\. ]$',
          '^\s+\(?\s*$');

}

1;
}
get_set_listsdescriptionprevnextTop
sub get_set_lists {
  return [["ExonerateGappedBest1", ["rattus_norvegicus","*"]]];
}
transcript_display_xref_sourcesdescriptionprevnextTop
sub transcript_display_xref_sources {
my @list = qw(RFAM
	      miRBase
	      HUGO
	      RGD
	      MGI
	      flybase_symbol
	      Anopheles_symbol
	      Genoscope_annotated_gene
	      Uniprot/SWISSPROT
Uniprot/
Varsplic RefSeq_peptide RefSeq_dna Uniprot/SPTREMBL
EntrezGene);
my %ignore; $ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted'; return [\@list,\%ignore];
}
General documentation
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