[Bioperl-l] motif features?

[shawnh@fugu-sg.org]

Cool I forgot about this. Yes its all based on bioperl. If its gonna get 
imported and exteneded beyond transfac, its got my vote and help if needed.


shawn



On Thu, 17 Oct 2002, Jason Stajich wrote:

> Mostly as features - Boris has written a TFBS finder which may eventually
> get imported into bioperl - would be good if we converge on an interface
> http://forkhead.cgb.ki.se/TFBS/
> 
> I think he basically has a TFBS::Site object for this which is essentially
> a SeqFeature with additional fields.
> 
> -j
> 
> # POD
> 
> =head1 NAME
> 
> TFBS::Site - a nucleotide sequence feature object representing (possibly
> putativ
> e) transcription factor binding site.
> 
> =head1 SYNOPSIS
> 
>     # manual creation of site object;
>     # for details, see documentation of Bio::SeqFeature::Generic;
> 
>     my $site = TFBS::Site
>                   (-start => $start_pos,     # integer
>                    -end   => $end_pos,       # integer
>                    -score => $score,         # float
>                    -source => "TFBS",        # string
>                    -primary => "TF binding site",  # primary tag
>                    -strand => $strand,       # -1, 0 or 1
>                    -seqobj => $seqobj,       # a Bio::Seq object whose
> sequence
>                                              #            contains the
> site
>                    -pattern => $pattern_obj  # usu. TFBS::Matrix:PWM obj.
> 
> -jason
> 
> On 18 Oct 2002, Shawn wrote:
> 
> >
> > Hi all,
> > 	I'm toying around with some motif finders mainly FootPrinter right now.
> > I was wondering whether there have been any work to represent
> > motifs in bioperl. Dugged around but I'm not sure that attaching
> > SeqFeatures to sequence would do the trick.
> >
> > Mainly what I would like to represent is that given n sequences, we
> > would have m different motifs (possibly overlapping) found across them.
> >
> > What I'm thinking of is to have some kinda
> > Bio::Seq::Motif or Bio::SeqFeature::Motif or Bio::Motif
> > that has a bunch of SeqFeatures attached to it representing
> > where this motif lies on the list of sequences.
> >
> > A use case:
> >
> > use Bio::SeqIO;
> > use Bio::Tools::Run::FootPrinter;
> >
> > my $sio = Bio::SeqIO->new(-file=>"seq.fa",-format=>"fasta");
> > my @seq;
> > while(my $seq = $sio->next_seq){
> > 	push @seq, $seq;
> > }
> >
> > my $fp = Bio::Tools::Run::FootPrinter->new();
> >
> > my @motif = $fp->run(@seq);
> >
> > foreach my $m (@motif){
> >  print $m->consensus."\n";
> >  foreach my $seqfeat($m->seqfeatures){
> >   print $seqfeat->seq_id."\t".$seqfeat->start."\t".$seqfeat->end."\n";
> >  }
> > }
> >
> > Other methods like
> >
> > $motif->information_content (bits)
> > $motif->pssm (weight matrix)
> > $motif->width
> > $motif->evalue etc...
> >
> >
> >
> > Throwing this out for discussion and half hoping someone's already done
> > something like that but I'm not finding it or that its a worthwhile
> > expedition.
> >
> >
> > cheers,
> >
> > shawn
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
> 
> 

-- 
********************************
* Shawn Hoon
* http://www.fugu-sg.org/~shawnh
********************************