Objective Given an input query, TErex1.0 identifies all the transposable elements within it through an alignment method that uses the Dfam database.
Significance Transposon annotation is an important tool because of the significance of transposable elements. Transposons are elements that move, or “jump around,” from one position to another within the genome, and they’re found abundantly in nearly all prokaryotes and eukaryotes. Consequently, transposable elements can lead to mutations, and recently, they’ve found a few transposons in cancer-related genes, indicating disease development. Because of their ability to “jump around,” transposons drive genomic evolution and gene regulation by enabling translocation, exon shuffling, and increasing diversity, among its many effects. Their genetic influence makes transposons important elements to identify and study.
- Clone the repository wherever you want to install the tools
- Run the following command to see if everything has been installed correctly!
python main.py --tester
Feel free to explore what our options do by running:
python main.py -h
Here's a list of dependencies that TErex requires to run!
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Python2.7
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Python package Numpy
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nhmmer through hmmer3.1
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perl
If you would like to download the whole Dfam database locally, you may use the link found here:
http://dfam.org/web_download/Current_Release/Dfam.hmm.gz