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General discussions (Q&As) / From DNA sequence to DNA structure
« on: November 18, 2009, 03:06:33 am »
Dear All,
I'm newbie in this field, however, I did not find any topic that can answer my question.
I want to study whether a pair of genes that separated by a distance of DNA sequence would close together in 3D conformation.
So, how to use 3DNA to generate a 3D DNA double-helix structure like this: http://http://hydra.icgeb.trieste.it/~kristian/dna/images/modelit_long2.jpg from a DNA sequence?
I've surveyed some tools like ADN-Viewer (not publicly available), model.it (can not accept long DNA).
And I've alos tried fiber, but all I got just a linear string of DNA structure like attached "Picture 1.png".
I know the "reconstruction function" in w3DNA provide a function: "Customized base-pair-step/nucleotide parameters".
But user seems have to provide all the parameters between every adjacent base pairs (dinucleotides): (example: http://http://w3dna.rutgers.edu/public/example/example_dna.txt)
So I think I need a set of general parameters to describe Shear, Stretch, Stagger, Buckle, Prop-Twist, Opening, Shift, Slide, Rise, Tilt, Roll, Twist for 16 dinucleotides.
There is a database called: DiProDB http://http://diprodb.fli-leibniz.de/ShowTable.php that already provides some parameters for dinucleotides.
Is 3DNA provide "general" parameters to reconstruct a naked double-strand DNA just like model.it did?
Thanks first.
I'm newbie in this field, however, I did not find any topic that can answer my question.
I want to study whether a pair of genes that separated by a distance of DNA sequence would close together in 3D conformation.
So, how to use 3DNA to generate a 3D DNA double-helix structure like this: http://http://hydra.icgeb.trieste.it/~kristian/dna/images/modelit_long2.jpg from a DNA sequence?
I've surveyed some tools like ADN-Viewer (not publicly available), model.it (can not accept long DNA).
And I've alos tried fiber, but all I got just a linear string of DNA structure like attached "Picture 1.png".
I know the "reconstruction function" in w3DNA provide a function: "Customized base-pair-step/nucleotide parameters".
But user seems have to provide all the parameters between every adjacent base pairs (dinucleotides): (example: http://http://w3dna.rutgers.edu/public/example/example_dna.txt)
So I think I need a set of general parameters to describe Shear, Stretch, Stagger, Buckle, Prop-Twist, Opening, Shift, Slide, Rise, Tilt, Roll, Twist for 16 dinucleotides.
There is a database called: DiProDB http://http://diprodb.fli-leibniz.de/ShowTable.php that already provides some parameters for dinucleotides.
Is 3DNA provide "general" parameters to reconstruct a naked double-strand DNA just like model.it did?
Thanks first.