[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);
$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
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