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README.md

Z-Hunt

Open the Notebook using this link Binder and open Tutorial.ipynb or Execute.ipynb.

Z Hunt Tutorial

This program was written in Python 3.6 using Jupyter Notebooks and displays a graphical interface for analyzing the data produced by Z-Hunt II, an updated version of Z-Hunt that analyzes a given DNA sequence and looks up for regions with potential to form Z-DNA. As mentioned by the authors:

" The computer program (Z-Hunt-II) developed for this study uses a rigorous thermodynamic search strategy to map the occurrence of left-handed Z-DNA in genomic sequences. The search algorithm has been optimized to search large sequences for the potential occurrence of Z-DNA, taking into account sequence type, length, and cooperativity for a given stretch of potential Z-DNA-forming nucleotides."

To do this the program computes for each base pair of the given DNA sequence, a value called Z-Score.

"In practical terms, the Z-Score relates the ability for a given sequence to adopt the Z conformation relative to a random sequence. We can also interpret the Z-Score as the number of random sequences that must be searched to find a nucleotide sequence that is as good or better at forming Z-DNA than the sequence in question."

Z-Hunt II accepts 5 arguments to run:

  • DNA: as a sequence made up A, T, G and C.
  • windowsize: the length of the search window.
  • minsize
  • maxsize
  • filename: the name of the text file with the results.

Using the user interface, these arguments are defined by changing the values inside of text windows. The default values of: windowsize, minsize and maxsize don't need to be necessarily changed by the user (they replicate correctly the results shown by the published articles). In the end, the program is very simple to use and requires the user to only input a DNA sequence and a name (for the results). The results can be explored in different ways by using buttons to call upon various functions.

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