[Biopython] Melting Point.TM_NN calculation

[Peter Cock]

Hi Ian,

I don't understand where the dot/period in '.G/AT' comes from.
Can you give some more details - a short script with the problem
sequences would be ideal.

In case it is relevant, which version of Biopython are you running?
(It looks like this is Python 2.7 under Apple OS X).

Peter

On Wed, Jun 24, 2015 at 3:39 PM, Ian Stavros <ianstavros at gmail.com> wrote:
> Hello,
>
> My name is Ian and I am new to the bioinformatics world. I am using the
> biopython's melting temp TM_NN algorithm to calculate the melting temp
> differences in wild type sequence with the complementary mutation sequence,
> using the the the Allawi and SantaLucia (1997), Biochemistry 36: 10581-10594
> table. I have attached a small output of the sample program for better
> understanding, which shows the Key Error I am getting and other times I will
> get a Value Error, meaning it can find the key but can't find the value, I
> was wondering if
>
> A) if there is something else out there better suited for this problem
>
> B) if I need to update the table or something to get working and if so how
> would I go about improving the dictionary being used to address the problems
> which can be seen here
>
>
> /Library/Python/2.7/site-packages/Bio/SeqUtils/MeltingTemp.py:931:
> BiopythonWarning: no data for neighbors 'AT/AG'. Calculation will be wrong
>   BiopythonWarning)
>
>
> Here is the output of the code. I think that the '.' may be equivalent to
> the regex expression of '.' meaning it could be any character in front of
> the G. But as you can see it is not a problem for the one up above.
>
>
> seq:  ['G', 'A', 'T']
> Mutation c_seq:  ['C', 'C', 'A']
> /Library/Python/2.7/site-packages/Bio/SeqUtils/MeltingTemp.py:931:
> BiopythonWarning: no data for neighbors 'AT/AG'. Calculation will be wrong
>   BiopythonWarning)
> TM:  -262.480685148
> seq:  ['G', 'A', 'T', 'A']
> Mutation c_seq:  ['C', 'C', 'A', 'T']
> Traceback (most recent call last):
>   File "PrimerBuilder.py", line 333, in <module>
>     switchList = switchBuilder(middle,basepairs,mutation)
>   File "PrimerBuilder.py", line 56, in switchBuilder
>     tmMismatch =
> mt.Tm_NN(switch,strict=False,c_seq=mutation,nn_table=mt.DNA_NN3)
>   File "/Library/Python/2.7/site-packages/Bio/SeqUtils/MeltingTemp.py", line
> 856, in Tm_NN
>     deltaH += de_table[right_de][dH]
> KeyError: '.G/AT'
>
>
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