This github respository contains source code and a binary for a modernized version of the algorithim Z-Hunt, now able to perform analysis of large genomic files in a user-friendly manner. It returns a "Z-Score" (not related to the common statistical Z-Score) for each nucleotide in a given sequence to rate the propensity of the 6-12 following nucleotides to convert to Z-Form, which is then paired with the location of the nucleotide in the genome and outputted as a BedGraph.
You can access a web interface for the program here:
http://dennis-hamrick.shinyapps.io/z-nome_hunt
If you are analyzing a large file or many files, it is recommended to use Z-NOME_HUNT locally. Z-NOME_HUNT runs as a command line interface tool. It takes four necessary arguments:
window_size : The size of the analysis window after a nucleotide. Larger values will take longer to run. Set this at 12.
min: Minimum window size acceptable for a Z-forming region. Set this at 6.
max: The maximum acceptable size for a z forming region. Larger deltas between minimum and maximum will increase the runtime. Set this at 12.
file-name: Your file of interest. See formatting notes.
and two optional arguments:
chromosome_name: The chromosome number or name your region of interest comes from.
start_site: The starting point for your sequence.
You can download an executable binary for your OS from the bin folder.
then
./z-nome_hunt 12 6 12 <your_file>
A new file will be created, .Z-SCORE.bedgraph. This can then be converted into a BigWig file by using bedgraphToBigWig or wigToBigWig.
By default, Z-NOME_HUNT assigns your filename (with .txt, .fa, or .fna extension removed) as the chromosome name in the output bedgraph file, and initializes start site as 0. If you want to run the algorithm with a different start site, use
./z-nome_hunt 12 6 12 <your_file> <chromosome_name> <start_site>
Download z-nome_hunt.c in zhunt_genome/source, then (if using gcc):
gcc -o z-nome_hunt z-nome_hunt.c -lm
The only information in the file should be its sequence. Downloaded chromosomes will usually have a first line with > then information. You can run
sed -i '1d' <yourfile>
in bash to remove this first line.
Formats besides these extensions or compressed sequence files may not work properly.
'N's in the genome and bases neighboring 'N's are assigned an arbitrary very low Z-Score. Z-scores for bases within 6-12 bases of an 'N' are therefore not trustworthy and should be ignored.
The original Z-HUNT and MZ-HUNT code that formed the basis for this project can be found here:
https://github.com/Ho-Lab-Colostate/zhunt/tree/master
Useful background reading can be found here:
https://github.com/Ho-Lab-Colostate/zhunt/tree/master/docs
https://link.springer.com/protocol/10.1007/978-1-0716-3084-6_14
This work is licensed under the MIT License. Full license information is available in LICENSE.md.