Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

A question about ntthal to cacualte "ANY" bounds between two oligos #64

Open
zenghp88 opened this issue Mar 11, 2022 · 0 comments
Open

Comments

@zenghp88
Copy link

zenghp88 commented Mar 11, 2022

When I run following command line with ntthal "ANY" mode, the result seems unreasonable.
./ntthal -a ANY -mv 50 -dv 1.5 -n 0.6 -d 50 -s1 ATTAGGAACCCACTCCCAAGATAAC -s2 GTTATCTAGGGAGTGGGTTTCTGAT
Calculated thermodynamical parameters for dimer: dS = -285.288 dH = -102700 dG = -14218 t = 46.3398

SEQ     ATT  G           AAGATAAC
SEQ        AG AACCCACTCCC
STR        TC TTGGGTGAGGG
STR     TAG  T           ATCTATTG

but in fact, it shoud be like this:

SEQ     ATT  G           A
SEQ        AG AACCCACTCCC AGATAAC
STR        TC TTGGGTGAGGG TCTATTG
STR     TAG  T           A

And I found that the value of "stackint2Enthalpies[3][0][0][0]" is "inf" which should be illogical. and it may lead to the unreasonable result above.
Both v2.5.0 and the latest version have been tested.

Best regards, Huaping Zeng

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant