[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome

Extract 3'UTR, 5'UTR, CDS, Promoter, Genes, Introns, Exons from GTF files

PromKappa 1.0 is a complete application made in Visual Basic 6.0 (VB6) that generates Objective Digital Stains (aka DNA patterns).

Bioinformatics N' Stuff

PromKappa 3.0 is a complete application made in Visual Basic 6.0 (VB6) that generates Objective Digital Stains (aka DNA patterns). The main output of the application consists of a series of images that are saved in the 'chart' (or 'chart_comp') folder and which can be later analyzed using different methods.

This repository contains custom code used for analysis in El Ghamrasni et al.,

Yeast pathway kit promoter and terminator vectors and other related public information. Do not put secret information here.

The Genomic Variations Explorer (GenVarX) is a toolset that consists of promoter region component and CNV component for users to perform queries, visualize data, and conduct annotations using genotypic and phenotypic differences.

The Soybean Genomic Variations Explorer (Soybean GenVarX) is a toolset that consists of promoter region component and CNV component for users to perform queries, visualize data, and conduct annotations using genotypic and phenotypic differences.

Workflow to identify functional cis-regulatory regions for each annotated cell type

Python second-order approximation to the PromoterHunter code