[Biopython] BioSeqUtilsMeltingTemp

[Peter Cock]

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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