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lib/Bio/Gonzales/Domain/Group.pm  view on Meta::CPAN

  return \@best_ones;
}

sub to_gff {
  my ( $self, $dest ) = @_;
  my $hits = $self->filter_hits;

  my $gffout = Bio::Gonzales::Feat::IO::GFF3->new( file_or_fh => $dest, mode => '>' );

  my $gidcs = $self->group_idcs;
  while ( my ( $d, $idx ) = each %$gidcs ) {
    $gffout->write_comment(" Group $idx contains domain: $d");
  }

  my $i = 0;
  for my $max (@$hits) {

    $gffout->write_feat(
      Bio::Gonzales::Feat->new(
        seq_id     => $max->{seq_id},
        source     => 'hmmer',

t/data/rprot-domains_ebakker.fasta  view on Meta::CPAN

>Nrg1-LRR  Required for N resistance in Nicotiana benthamiana gi|66737320|gb|AAY54606.1|
LKTLIVANNYFFPTKLNNFQLCSLLNLKRISLERISVTSIFTANLQLPNLRKISFIMCEIGEAFENYAANMSYMWPKLVEMNIEYCSDLVEVPAETCDLVGLKKLSICYCHELVALPEELGKLSNLEVLRLHSCTNVSKLPESVVKLNRLGFLDVYDCVELDFLPREMDQLCSLRTICMGSRLGFTELPDSVLRLVKLEDVVCDEETASLWEYYKEHLRNLRITVIKEDINLNLLHKSLFI
>RRS-1-TIR Resistance to Ralstonia solanacearum in Arabidopsis thaliana gi|76803833|sp|Q9FH83.3|
MTNCEKDEEFVCISCVEEVRYSFVSHLSEALRRKGINNVVVDVDIDDLLFKESQAKIEKAGVSVMVLPGNCDPSEVWLDKFAKVLECQRNNKDQAVVSVLYGDSLLRDQWLSELDFRGLSRIHQSRKECSDSILVEEIVRDVYETHFYVGRIGIYSKLLEIENMVNKQPIGIRCV
>RRS-1-NBS Resistance to Ralstonia solanacearum in Arabidopsis thaliana gi|76803833|sp|Q9FH83.3| GIWGMPGIGKTTLAKAVFDQMSSAFDASCFIEDYDKSIHEKGLYCLLEEQLLPGNDATIMKLSSLRDRLNSKRVLVVLDDVRNALVGESFLEGFDWLGPGSLIIITSRDKQVFCLCGINQIYEVQGLNEKEARQLFLLSASIKEDMGEQNLQE...
>RRS-1-LRR Resistance to Ralstonia solanacearum in Arabidopsis thaliana gi|76803833|sp|Q9FH83.3|
EIEGLFLDTSNLRFDLQPSAFKNMLNLRLLKIYCSNPEVHPVINFPTGSLHSLPNELRLLHWENYPLKSLPQNFDPRHLVEINMPYSQLQKLWGGTKNLEMLRTIRLCHSHHLVDIDDLLKAENLEVIDLQGCTRLQNFPAAGRLLRLRVVNLSGCIKIKSVLEIPPNIEKLHLQGTGILALPVSTVKPNHRELVNFLTEIPGLSEELERLTSLLESNSSCQDLGKLICLELKDCSCLQSLPNMANLDLN...
>N-Nt-TIR Resistance to TMV in Nicotiana tabacum gi|45544513|dbj|BAD12594.1| 
massssssrwsydvflsfrgedtrktftshlyevlndkgiktfqddkrleygatipgelckaieesqfaivvfsenyatsrwclnelvkimecktrfkqtvipifydvdpshvrnqkesfakafeehetkykddvegiqrwrialneaanlkgscdnrdktdadc
>N-Nt-NBS Resistance to TMV in Nicotiana tabacum gi|45544513|dbj|BAD12594.1| 
irqivdqissklckislsylqnivgidthlekieslleigingvrimgiwgmggvgkttiaraifdtllgrmdssyqfdgacflkdikenkrgmhslqnallsellrekanynneedgkhqmasrlrskkvlivlddidnkdhyleylagdldwfgngsriiittrdkhliekndiiyevtalpdhesiqlfkqhafgkevpnenfeklslevvnyakglplalkvwgsllhnlrltewksaiehmknns...
>N-Nt-LRR Resistance to TMV in Nicotiana tabacum gi|45544513|dbj|BAD12594.1| 
msnntgtmameaiwvssysstlrfsnqavknmkrlrvfnmgrssthyaidylpnnlrcfvctnypwesfpstfelkmlvhlqlrhnslrhlwtetkhlpslrridlswskrltrtpdftgmpnleyvnlyqcsnleevhhslgccskviglylndckslkrfpcvnvesleylglrscdsleklpeiygrmkpeiqihmqgsgirelpssifqykthvtklllwnmknlvalpssicrlkslvslsvsgc...
>N-Nt-CNL Resistance to TMV in Nicotiana tabacum gi|45544513|dbj|BAD12594.1| 
lsltvftgqpypekipswfhhqgwdssvsvnlpenwyipdkflgfavcysrslidttahlipvcddkmsrmtqklalsecdtessnysewdihfffvpfaglwdtskangktpndygiirlsfsgeekmyglrllykegpevnallqmrensneptehstgirrtqynnrtsfyeling
N-Lu-TIR (Lu)>gi|13509207|emb|CAC35321.1| Ngc-D protein [Linum usitatissimum]
MMRSDSNGSTDSFHSCSSADLTFPPLPSGEYEVFLSFRGPDVRKTFADHLYTSLVRSKFRTFRDEEELEKGGTIGPSLIRAITESKIYIPILTPNYASSKWCLQELAKMVGCWKSGGGAKGQHIILPVFLFVDPRDVRHTESGSYKEAFEEHSQKHDPETVLEWKEALQEVGEMKGYHVTESDG
N-Lu-NBS (Lu)>gi|13509207|emb|CAC35321.1| Ngc-D protein [Linum usitatissimum]
HGSIIDKILTEVELHLGANYALVTDELVGIDSRVDEVVGLLNLDSSTSEKIIGIHGMGGLGKTTLAKAVYDKVSTKFERCYFLENIRDTLSEKNGVSILQNKIISGILRKDFNEAKNASDGIRIIRDRVCRHKLLIVLDDVDEKFQFDDVLGKLNNFSTNSRFLITTRDARGLELLQEYKMFELQEMSPDHSLTLFNKHAFDVDCPPKDYAILSKEFVQAAAGLPLYIKVIGSLLFRMDKIFWEEKLEEF...
N-Lu-LRR (Lu)>gi|13509207|emb|CAC35321.1| Ngc-D protein [Linum usitatissimum]
GTDCVEVLTVDMEGEDLILTNKEFEKLTMLRYLKVSNARLAGDFKDVLPNLRWLLLESCDSVPSGLYLKKLVRLDLHDCSVGDSWKGWNELKVARKLKAVSLKRCFHLKKVPDFSDCGDLEFLNFDGCRNMRGEVDIGNFKSLRFLYISKTKITKIKGEIGRLLNLKYLSVGDSSLKEVPAGISKLSSLEFLALALTDSYKSDFTEMLPTSLTLLYISNDTQKFCPDTSSENLQRLPNLSNLINLSVLYL...