[meltsim] Re: MELTSIM

[Taofiq Paraiso]

Dear Richard Blake,
I am using Meltsim in order to study the dependance of dna melting 
curves with respect to
loop exponent and cooperativity parameter.
I would like to know where they can be modified in the code.
Many thanks and best regards,

Taofiq Paraiso


J.W. Bizzaro wrote:

> Hi Taofiq.
>
> Questions about the algorithm will be best answered by Richard Blake.
> Please send your question to <meltsim at bioinformatics.org> asking him
> specifically.
>
> Do you have Enrico Carlon's email address?
>
> Cheers.
> Jeff
>
> Taofiq Paraiso wrote:
>
>> Hi Jeff,
>>
>> Finally my administrator could modify the code in order to run it 
>> under Linux.
>> We don't have the user interface any more but this is not a problem.
>> Now I would like to modify the loop exponent and cooperativity 
>> parameters, which are
>> called alpha and sigma in the code respectively.
>> I understood that the value of alpha was assumed to be 1.75 (alpha is 
>> not initialized in the code).
>> The value of sigma is calculated according to initial and the final 
>> values of sigma, which seem
>> to be in relation with the initial and final temperature. Could you 
>> confirm if I understood well?
>>
>> Best regards, Tao
>>
>> ps: I just received an email from Enrico Carlon, who told me that he 
>> has a C version of meltsim.
>
>