[Biopython] BioSeqUtilsMeltingTemp

[Stefanie Lück]

Hi Peter,

yes it is exactly! Unfortunately Markus and Jennifer discussed and solved
it separately.

Thanks
Stefanie


2016-01-19 10:20 GMT+01:00 Peter Cock <p.j.a.cock at googlemail.com>:

> Hi Stefanie,
>
> This sounds very similar to this issue - is it?:
> https://github.com/biopython/biopython/issues/682
>
> Peter
>
> On Tue, Jan 19, 2016 at 7:52 AM, Stefanie Lück <luecks at gmail.com> wrote:
> > Hello everybody!
> >
> > First of all I would like to thank you because of the great
> documentation of
> > the module I mention above.
> >
> > However I have a problem. I am trying to calculate the temperature with
> > Tm_NN by using dangling ends.
> >
> > I am calling the function like this:
> >
> > Tm_NN(seq, check=True, strict=True, c_seq=c_seq, shift=1,
> nn_table=RNA_NN3,
> >           tmm_table=DNA_TMM1, imm_table=DNA_IMM1, de_table=RNA_DE1,
> >           dnac1=25, dnac2=0, selfcomp=False, Na=20, K=50, Tris=0, Mg=0,
> >           dNTPs=0, saltcorr=5)
> >
> > whereas an example,
> >
> > seq = GAT
> > c_seq = TCTA
> >
> > which means:
> > -GAT
> > TCTA
> >
> > Unfortunately I got a keyerror (KeyError: '.G/TC') because the dictionary
> > does not contain '.G/TC' but 'CT/G.'
> >
> > Do I have to supply the two sequences in a different way? I can not find
> > what I am doing wrong, I supply seq in 5'-3' and c_seq in 3'-5'
> direction.
> >
> > Any help would be very appreciated!
> > Thanks,
> > Stefanie
> >
> > _______________________________________________
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> > http://mailman.open-bio.org/mailman/listinfo/biopython
>
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