[Bioperl-l] Build new Swiss-Prot Seq

Brian Osborne brian_osborne at cognia.com
Thu Sep 16 08:16:59 EDT 2004


I'm not sure I understand. Are you seeing errors when you run your code?

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: Thursday, September 16, 2004 8:00 AM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] Build new Swiss-Prot Seq

Hello , everybody can help me, i want to buid a new
sequence in swissprot and i have used  3 modul such as
Bio::SeqFeature, Bio::Seq, Bio::Annotation::Comments,
Bio::Annotation::Simplevalue, Bio::Annotation
Bio::Annotation::references and
Bio::Annotation::Dblink,  so it's true or not.

This is my souces code;

$feat = new Bio::SeqFeature::Generic ( -start => 10,
-end => 100,
                                -strand => -1,
-primary => 'repeat',
                                -source_tag   =>
                                -display_name => 'alu
                                -score  => 1000,
                                -tag    => {
                                    new => 1,
                                    author =>
                                    sillytag => 'this
is silly!' } );

#my $feat = new Bio::SeqFeature::Generic(-start
=>10,-end => 22, -strand =>1,
#                                       -tag =>{
author => 'john',note =>'TATA box'});

$feat->add_tag_value("match1","PF000123 e-7.2");
$feat->add_tag_value("match2","PF002534 e-7.2");

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

my $seq_obj =Bio::Seq
-display_id=>"BIO52" );

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

  my $col = new Bio::Annotation::Collection;
   my $sv = new Bio::Annotation::SimpleValue(-value =>
   $col->add_Annotation('tagname', $sv);

    $reg = Bio::Annotation::Reference->new( -title =>
'title line',
=> 'location line',
=> 'author line',
=> 998122 );

 $link1 = new Bio::Annotation::DBLink(-database =>
                                        -primary_id =>


   $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

$feat->annotation->add_Annotation('dblink', $link2);


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

$io ->write_seq($seq_obj);

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