Data / Code

Links to our chromosome data set and source codes for all programs. CUDA-compatible GPUs are necessary to run the programs. Programs can run in most IDEs, but were developed in Microsoft Visual Studio 2022. See the README here.

Generate SEQSIM compatible files from FASTA

Download FASTA sequence files from genome browser and related sites and use this code to generate SEQSIM compatible TXT files.

SEQSIM - CUDA Optimized, 2-Input

Generate .CSV files and full similarity matrices from sequence TXT files. Teh file allows you to select a range you wish to analyze (2-Input)

HeatMap Creator

Generate BMP Heatmap files from CSV outputs from the main SEQSIM program.

BMP Upscale

Increase the size of your heatmap BMPs for visual/analytical purposes or generating figures.

CSV to CONTACTS

Generate a .CONTACTS file to use with CSynth from the SEQSIM output CSV file.

Original Dataset Download

Contact us if you wish to receive the entire CSV dataset generated with SEQSIM for Chr1-24. The dataset is ~2 GB. Below is a link to the CSV heatmaps.

View the BMP Heatmaps

Get in Touch

Having issues? Contact us!