None available.
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; } |
sub get_set_lists
{
return [["ExonerateGappedBest1", ["rattus_norvegicus","*"]]]; } |
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]; } |