[meltsim] Re: Question regarding MeltSim

[R. D. Blake]

Jeff,
Ah! I should have read this message first. I essentially told her the 
same as you did. She is apparently working with a short and somewhat 
neighbor-biased sequence.

At 05:56 PM 3/21/2006, you wrote:

>Hi Christine,
>
>MeltSim's empirical parameters include stability parameters for all 
>16 nearest-neighbor pairs (instead of the 10 unique pairs), which 
>are all assumed to be on the same strand.  From the source code:
>
>#define GG_STAB salt_log10 * 14.18 + 391.65
>#define CC_STAB salt_log10 * 14.18 + 391.65
>#define GC_STAB salt_log10 * 13.20 + 397.77
>#define CG_STAB salt_log10 * 13.20 + 397.70
>#define AC_STAB salt_log10 * 16.21 + 381.12
>#define GT_STAB salt_log10 * 16.21 + 381.12
>#define CA_STAB salt_log10 * 17.10 + 376.34
>#define TG_STAB salt_log10 * 17.10 + 376.34
>#define AG_STAB salt_log10 * 16.87 + 377.59
>#define CT_STAB salt_log10 * 16.87 + 377.59
>#define GA_STAB salt_log10 * 17.76 + 372.65
>#define TC_STAB salt_log10 * 17.76 + 372.65
>#define AT_STAB salt_log10 * 21.00 + 355.01
>#define TA_STAB salt_log10 * 20.11 + 359.88
>#define AA_STAB salt_log10 * 19.78 + 362.24
>#define TT_STAB salt_log10 * 19.78 + 362.24
>
>But, since an "AT" NN pair, for example, has a different stability 
>than the reverse "TA" NN pair, you'll get different amplitudes 
>(albeit somewhat similar features) between derivative plots, 
>depending on the direction in which the sequence is read.
>
>Notice, though, that the stability parameters are the same between 
>NN pairs that are the reverse *complement* of each other, meaning it 
>doesn't matter which strand you use.
>
>Cheers,
>Jeff
>
>Christine Kingsburry wrote:
>>Hi,
>>My name is Christine Kingsburry and I'm working in Gary Slater's group at
>>the University of Ottawa, Canada.  We recently got interested in DNA
>>melting and in your program MeltSim.  We noticed that there is discrepancy
>>between the curves obtained for the same DNA sequence, but in the inverse
>>form.  We were just wondering if you knew the reason why.  Is it a 3' 5'
>>effect?
>>Thank you
>>Christine
>
>--
>J.W. Bizzaro
>Bioinformatics Organization, Inc. (Bioinformatics.Org)
>E-mail: jeff at bioinformatics.org
>Phone:  +1 508 890 8600
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