[Bioperl-l] Secondary structure prediction

Richard Adams Richard.Adams at ed.ac.uk
Thu Aug 5 11:57:56 EDT 2004

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);
  print $sopma->result;# #raw text to standard error
my @fts = $tool->result('Bio::SeqFeatureI');

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. 



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

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

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