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Questions and answers => General discussions (Q&As) => Topic started by: mikeshelk on August 25, 2010, 07:05:00 am

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Title: What do numbers in *.inp files mean?
Post by: mikeshelk on August 25, 2010, 07:05:00 am
Dr. Xiang-Jun, hello!
I would like to ask about the find_pair output
Consider a string "
  194  239  0 #    5 | -:...5_:[..T]T-----A[..A]:..23_:-  0.32  0.17 17.11  8.91 -0.83
"
Could you please tell me what all five numbers in "0.32  0.17 17.11  8.91 -0.83" exactly mean?

Thanks
Mikhail Schelkunov
Title: Re: What do numbers in *.inp files mean?
Post by: xiangjun on August 26, 2010, 12:06:32 am
Well, this is a clearly defined question with a concrete example  and I am in a unique position to answer it  :) .

Quote
Could you please tell me what all five numbers in "0.32 0.17 17.11 8.91 -0.83" exactly mean?
The content after the # sign is not documented because it was initially used for debugging purpose only. Since you asked, here is a brief account of what the five numbers mean, using your specified example with unit in () at the end:

Overall, the first four numbers are for identifying a base pair, while the fifth number is for checking its inclusion/exclusion in a duplex.

Over the years, [mono:3bemt574]find_pair[/mono:3bemt574] has turned out to be an essential 3DNA application that makes analyzing nucleic acid structure straightforward.  See my blog post "What find_pair in 3DNA can do (http://http://xiang-jun.blogspot.com/2010/03/what-findpair-in-3dna-can-do.html)". As I've mentioned in several occasions, a detailed account of the underlying algorithm of  [mono:3bemt574]find_pair[/mono:3bemt574] has still to be written. I've been continuously refining [mono:3bemt574]find_pair[/mono:3bemt574] internally, and hopefully I will be able to write a paper on it in the not too distant future.

HTH,

Xiang-Jun

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.