[Bioperl-l] Tm calculation

Sebastian Bassi sbassi at asalup.org
Thu Feb 19 21:25:14 EST 2004


I suscribed to this list because I was told there is a thread about Tm. 
I did a Tm function for Biopython, based on the EMBOSS DAN. The good 
thing is that it performed exactly as DAN. The problem was that DAN 
formulae was dated (it was previous to Santalucia work).

I have some questions:
-Regarding "#$entropy -= 1.4; #Should only be applied to 
self-complimentary oligos, so add code to test self complimentarity 
before applying this line to Tm calculations "
How do you define self complementary oligos?
Is this a self complementary oligo: AAACCCTAGGGTTT? What about this: 
-Does the proposed version test for overriding pairs? I mean, take this 
sequence: ACCCGTGAGCTG. How many CC pairs that the program detects? The 
right anwser should be 2. But if you are using a standard string find 
function, it may overlook the overrriding CC and detect only one. I had 
this problem in one of my atemps. So I had to made my own find string 
function (somebody from biopython mailing list coded this function at my 
request, so I didn't actually wrote it).

I'm asking this instead of looking at the code because I don't know 
enought Perl (that's why I work on Python :)

Sorry for my English, it is not my native languaje!

Best regards,

//=\ Sebastian Bassi - Diplomado en Ciencia y Tecnologia, UNQ   //=\
\=// IT Manager Advanta Seeds - Balcarce Research Center -      \=//
//=\ Pro secretario ASALUP - www.asalup.org - PGP key available //=\
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