Welcome to the help page of Segmentron! Segmentron is a python library (PyPI Link) developed by the Regev Lab at NYU in collaboration with the Boeke Lab at NYU Langone for calculating the optimal segmentation of DNA for synthesis by yeast. Users are able to adjust what parameters are considered in the segmentation process according to their needs.
Example Snapgene Input: HLA2_Sergio_test.dna
Have the DNA sequence written in Nucleotides ATCG.
Example Text Input: HLA2_Sergio_test.txt
Example FASTA Input: HLA2_Sergio_test.fa
There are currently three different output options/formats.
The text output conists of the range of indicies [start, end] from the original sequence that each segment contains as well as the nucleotides themselves. These segments have the overlap included and can be used to produce the segments directly.
Example Text Output: HLA2_Sergio_Test_segmentation_results_txt.txt
This .bed output consists of the endpoint indices of each segment. When opened in snapgene alongisde the original DNA sequence one can observe the segmentation
Example Bed Output: HLA2_Sergio_Test_segmentation_results_bed.bed
The .bed output including forbidden regions consists of the endpoint indices of each segment as well as the endpoint indices of all the forbidden regions that were incorporated into the calculation. When opened in snapgene alongisde the original DNA sequence one can observe the segmentation as well as user-specified and generated forbidden regions
Example Bed + Forbidden Regions Output: HLA2_Sergio_Test_segmentation_results_bedFR.bed
The process may take long, so please be patient!
We have developed a Python library called Segmentron which provides an API for users to segment given a target DNA Sequence and a variety of parameters. We utilize Pyodide to compile and run Python code using the Segmentron library into Web Assembly.
To run NIH's BLAST we create utilize a v86 container to run a Debian Disk Image with a precompiled version of BLAST.
We utilize a WebWorker which is a Javascript Script which runs in the background. This enables the UI on the main thread to be interactive whilst we are running intensive computations like Segmentron or BLAST.