[Bioperl-l] Secondary structure prediction

[Richard Adams]

Hi Jon,
One way is to use the Bio::Tools::Analysis::Protein::HNN/Gor4/Sopma 
module e.g.,

e.g., if you have a Bio::Seq object, $seq

 my $sopma = Bio::Tools::Analysis::Protein::Sopma->new
      		(-seq=>$seq, states=>4);
  $sopma->run;
  print $sopma->result;# #raw text to standard error
my @fts = $tool->result('Bio::SeqFeatureI');
$seq->add_SeqFeature(@fts);	

will submit the sequence to the analysis, run remotely, and return the results as sequence features.
This is described more fully in the SimpleWebAnalysis HOWTO document. 

There is also an EMBOSS program garnier which can be wrapped using the Bio::Tools::EMBOSS module. 

HTH
Richard


  



-- 
Dr Richard Adams
Psychiatric Genetics Group,
Medical Genetics,
Molecular Medicine Centre,
Western General Hospital,
Crewe Rd West,
Edinburgh UK
EH4 2XU

Tel: 44 131 651 1084
richard.adams at ed.ac.uk