[Bioperl-l] Build new Seq in SwissProt

Brian Osborne brian_osborne at cognia.com
Mon Sep 20 09:21:55 EDT 2004


The DT Annotation is made by constructing a Bio::Annotation::SimpleValue

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of hafiz hafiz
Sent: Saturday, September 18, 2004 6:04 AM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] Build new Seq in SwissProt

hello, help me, which bioperl modul should we use to
insert Date  in swiss prot?


ID   GRAA_HUMAN     STANDARD;      PRT;   262 AA.
AC   P12544;

this date i mean
DT   01-OCT-1989 (Rel. 12, Created)
DT   01-OCT-1989 (Rel. 12, Last sequence update)
DT   28-FEB-2003 (Rel. 41, Last annotation update)

my soure code; any suggestion

my $feat = new Bio::SeqFeature::Generic(-start
=>10,-end => 22, -strand =>1,-primary =>"DOMAIN");

#my @arr = $feat->get_all_tags;
#for my $tag (@arr){
#       print $tag,":",$feat->get_tag_values($tag),"

my $seq_obj =Bio::Seq
=>"BIO52",-accession_number =>
'X78121',-alphabet => 'dna',-is_circular => 1);


my $comment =Bio::Annotation::Comment->new;
$comment->text("this looks like a good TATA box");
my $coll =new Bio::Annotation::Collection;

$species = Bio::Species->new(-classification =>
           # Can also pass classification
           # array to new as below
 $species->classification(qw( sapiens Homo Hominidae
                                 Catarrhini Primates
                                 Mammalia Vertebrata
                                 Metazoa Eukaryota ));

    $genus = $species->genus();

    $bi = $species->binomial();     # $bi is now "Homo

    # For storing common name

    # For storing subspecies
my $reg = Bio::Annotation::Reference->new(  -title
=>"SwissProt Data",
=> "Gerik" ,
=>"Muhammad hafiz Mohamed Yusof",
=> "998122",-comment=>"sdasd",-position=>"sdsadd" );


$link2 = new Bio::Annotation::DBLink();

   # DBLink is-a Bio::AnnotationI object, can be added
to annotation
   # collections, e.g. the one on features or seqs


my $io= Bio::SeqIO ->new(-format =>"swiss",-file =>

$io ->write_seq($seq_obj);

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