[Bioperl-l] Secondary structure prediction
Richard.Adams at ed.ac.uk
Thu Aug 5 11:57:56 EDT 2004
One way is to use the Bio::Tools::Analysis::Protein::HNN/Gor4/Sopma
e.g., if you have a Bio::Seq object, $seq
my $sopma = Bio::Tools::Analysis::Protein::Sopma->new
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,
Molecular Medicine Centre,
Western General Hospital,
Crewe Rd West,
Tel: 44 131 651 1084
richard.adams at ed.ac.uk
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