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Shouldn't stackmm value for TA_AA be 4700 instead of inf? #35

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Curley-Joe opened this issue Mar 19, 2020 · 2 comments
Open

Shouldn't stackmm value for TA_AA be 4700 instead of inf? #35

Curley-Joe opened this issue Mar 19, 2020 · 2 comments

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@Curley-Joe
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The ds value for stackmm AA_AT is 4700, which seems correct, but the dh value for TA_AA is "inf" due to commit 8c2aa69. I think the value for TA_AA should have been left at 4700.
@Curley-Joe Curley-Joe changed the title Shouldn't stackmm value for AT_AA be 4700 instead of inf? Shouldn't stackmm value for TA_AA be 4700 instead of inf? Mar 19, 2020
@untergasser
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Hi,
we try to trace back what lead to this changes. Can you provide more information why this change was incorrect?
Best,
Andreas

@Curley-Joe
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It was a long time ago that I reported this, so my memory is faint, but I think I was looking at the SantaLucia papers and they have 4.7 for AA_AT dh. See "Nearest-Neighbor Thermodynamics and NMR of DNA Sequences with Internal
A-A, C-C, G-G, and T-T Mismatches".

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@Curley-Joe @untergasser