[Fwd: Re: [Bioperl-l] Bio::SeqFeature::Primer Calculating the Primer TM]

[Barry Moore]

Sebastian,

These lines account for initiation of duplex formation:

 #Account for initiation parameters
 $enthalpy += $thermo_values{substr($sequence, 0, 1)}{enthalpy};
 $entropy += $thermo_values{substr($sequence, 0, 1)}{entropy};
 $enthalpy += $thermo_values{substr($sequence, -1, 1)}{enthalpy};
 $entropy += $thermo_values{substr($sequence, -1, 1)}{entropy};

However your question made me go back and look at the 1997 and 1998 
SantaLucia papers again, and I realized that I have applied the symmetry 
correction incorrectly.  Symmetry correction should only be applied to 
self complimentary oligos.  The code could be modified to identify these 
and apply symmetry correction, but short of that the correction should 
probably just be  removed since most oligos (especially ones used in 
molecular biology) won't be self complimentary.  Rob, that could be 
fixed by replacing this line:

 $entropy -= 1.4;

with something like this line:

 #$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

Barry Moore
Dept. Human Genetics
University of Utah

Sebastian Bassi wrote:

> Barry Moore wrote:
>
>> Sebastian,
>>
>> You may have picked this up from the bioperl list if  you follow 
>> that, but since it sounded like you were on the python side, I 
>> thought I'd pass it along.
>
>
> Yes. I am working on this in BioPython.
> What it seems this code is lacking is some correction for "douplex 
> inicialization". That is stated in Santalucia paper.
>