[BioRuby] Melting Temperature

Rob Syme rob.syme at gmail.com
Thu Oct 9 18:08:41 UTC 2014


That implementation looks more sensible to me.
-r

On Thu, Oct 9, 2014 at 1:21 PM, Naohisa Goto <ngoto at gen-info.osaka-u.ac.jp>
wrote:

> Hi,
>
> I've found another implementation to calculate Tm in a blog:
> http://d.hatena.ne.jp/fukuit/20101022/1287765340
> Although the blog is written in Japanese, the Ruby code is clear.
> The code resembles with Bioroebe's code because the same formula
> is used to calculate Tm.
>
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
>
> > Hi David
> >
> > The 'bioroebe' gem includes Tm calculation.
> >
> >     $ gem install bioroebe
> >     $ irb
> >
> >     > require 'bioroebe/calculate_melting_temperature'
> >     > seq = 'ATGCTGACGTATGCGATCGTA'
> >     > tm = CalculateMeltingTemperature.new
> >     > tm.set_input(seq)
> >     > tm.calculate_tm
> >     # ==> 65.32166985617363
> >
> > You can set oligo nucleotide concentration, Na+ conc and
> > formamide_concentration.
> >
> > The method isn't too complicated
> > <
> http://rubydoc.info/gems/bioroebe/0.0.44/CalculateMeltingTemperature:calculate_tm
> >
> >
> > Rob Syme
> >
> > On Thu, Oct 9, 2014 at 6:10 AM, McCreavy David <
> David.McCreavy at lhch.nhs.uk>
> > wrote:
> >
> > > Hi Guys,
> > >
> > > Where in the API will I find methods for calculating Tm?
> > >
> > > Kind Regards, David
> > >
> > >
> > >
> > >
> > >
> > >
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