Bio-GeneDesign

 view release on metacpan or  search on metacpan

lib/Bio/GeneDesign.pm  view on Meta::CPAN

The -sequence argument is required.

Returns the melting temperature of a DNA sequence.

You can set the salt and DNA concentrations with the -salt and -concentration
arguments; they are 50mm (.05) and 100 pm (.0000001) respectively.

You can pass either a string variable, a Bio::Seq object, or a Bio::SeqFeatureI
object to be analyzed with the -sequence flag.

There are four different formulae to choose from. If you wish to use the nearest
neighbor method, use the -nearest_neighbor flag. Otherwise the appropriate
formula will be determined by the length of your -sequence argument.

For sequences under 14 base pairs:
  Tm = (4 * #GC) + (2 * #AT).

For sequences between 14 and 50 base pairs:
  Tm = 100.5 + (41 * #GC / length) - (820 / length) + 16.6 * log10(salt)

For sequences over 50 base pairs:
  Tm = 81.5 + (41 * #GC / length) - (500 / length) + 16.6 * log10(salt) - .62;



( run in 0.821 second using v1.01-cache-2.11-cpan-3cd7ad12f66 )