[Bioperl-l] Calculating Tm for nucleotides

Rob Edwards redwards at utmem.edu
Thu Jun 3 16:34:36 EDT 2004

If you want to use BioPerl, check out Bio::SeqFeature::Primer

Make sure that you have a recent version of BioPerl that has the 
changes suggested by Barry Moore (he should be credited in the file).

This may not be the quickest, but it will work!

For example:

use Bio::SeqFeature::Primer;
foreach my $seq (@seqs) {
  my $primer=Bio::SeqFeature::Primer->new(-seq=>$seq);
  print "$seq\t", $primer->Tm, "\n";

or, assuming one primer per line in a file:

perl -MBio::SeqFeature::Primer -ne 'chomp; 
$p=Bio::SeqFeature::Primer->new(-seq=>$_); print "$_\t", $p->Tm, "\n"' 


On Jun 3, 2004, at 2:53 PM, Sean Davis wrote:

> All,
> I am interested in calculating Tm for oligos (many thousands of them). 
>  What
> is the fastest way of doing this?  I see at least two ways (emboss and
> primer.pm and there are probably more).
> Thanks,
> Sean
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> Bioperl-l at portal.open-bio.org
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