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lib/InSilicoSpectro/Databanks/DBEntry.pm  view on Meta::CPAN

=head3 $dbe->sequence([val])

Get/Set AC, ID, ...

=head3 $dbe->seqType(["AA"|"DNA"])

Get or set the sequence type

=head3 $dbe->annotatedModRes(string|[[pos1, mod1], [pos2, mod2]]);

get or set annotated PTM from a string (e.g. (1|ACET_nterm)(2|ACET_nterm)(185|PHOS)) or an array. All previously set TPM are removed

=head3 $dbe->add_annotatedModRes(pos, modkey)

add an annotated PTM

=head3 $dbe->clear_annotatedModRes()

remove all annotated modres

=head3 $dbe->variants(string|[[pos1, seq1a, seq1b], [pos2, seq2a, seq2b]]);

t/DBEntry.t  view on Meta::CPAN

my $dir=dirname $0;

chdir $dir;

use InSilicoSpectro::Databanks::DBEntry;

my $dbe=InSilicoSpectro::Databanks::DBEntry->new;
ok($dbe, "InSilicoSpectro::Databanks::DBEntry object instanciated");

my $str=<<'EOT';
>P68250_CHAIN0 \ID=1433B_BOVIN \ACOR=P68250 \DE=14-3-3 protein beta/alpha (Protein kinase C inhibitor protein 1) (KCIP-1) \NCBITAXID=9913  \MODRES=(1|ACET_nterm)(2|ACET_nterm)(185|PHOS)   \VARIANT= \LENGTH=245
TMDKSELVQK AKLAEQAERY DDMAAAMKAV TEQGHELSNE ERNLLSVAYK NVVGARRSSW
RVISSIEQKT ERNEKKQQMG KEYREKIEAE LQDICNDVLQ LLDKYLIPNA TQPESKVFYL
KMKGDYFRYL SEVASGDNKQ TTVSNSQQAY QEAFEISKKE MQPTHPIRLG LALNFSVFYY
EILNSPEKAC SLAKTAFDEA IAELDTLNEE SYKDSTLIMQ LLRDNLTLWT SENQGDEGDA
GEGEN
EOT

$dbe->AC('POUET');

$dbe->readFasta($str);

t/insilicodef-test.xml  view on Meta::CPAN

    <oneInternFragType name="immo">
      <residues>HFILYPV</residues>
      <delta monoisotopic="-26.9871" average="-26.9871"/>
    </oneInternFragType>
  </internalFragType>

 </fragTypeDefSet>
</fragTypeDescriptions>

<modRes>
  <oneModRes type="ptm" name="ACET_nterm">
    <description>Acetylation_nterm</description>
    <site>
      <residue>^NKHFW</residue>
      <nterm/>
    </site>
    <residues aa="^NKHFW" nterm="yes"/>
    <delta monoisotopic="42.0106" average="42.0373"/>
    <sprotFT><![CDATA[(N-acetylalanine|N-acetylaspartate|N-acetylcysteine|N-acetylglutamate|N-acetylglycine|N-acetylmethionine|N-acetylproline|N-acetylserine|N-acetylthreonine|N-acetyltyrosine|N-acetylvaline).*]]></sprotFT>
  </oneModRes>
  <oneModRes type="ptm" name="ACET_core">
    <description>Acetylation_core</description>
    <site>
      <residue>KR</residue>
    </site>
    <residues aa="KR"/>
    <delta monoisotopic="42.0106" average="42.0373"/>
    <sprotFT><![CDATA[(N2-acetylarginine|N6-acetyllysine).*]]></sprotFT>
  </oneModRes>
  <oneModRes type="ptm" name="PHOS">
    <description>Phosphorylation</description>