[Biopython] Melting Point.TM_NN calculation

[Ian Stavros]

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'
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20150624/6dc82fef/attachment.html>