promoter

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

Django app for managing referral programs — promoters, referral tracking, commission payouts, Wise CSV export, and click analytics.

Machine-learning-based general bacterial promoter prediction tool.

PARE: a computational method to Predict Active Regulatory Elements

Find two-boxes transcription factor binding sites (made for sigma factor binding sites) by comparing intergenic DNA regions upstream pairs of orthologous genes using statistical analyses

Sigma70Pred: A highly accurate method for predicting sigma70 promoter in Escherichia coli K-12 strains

extract promoter sequence from A.thalian genome

As a cell-free DNA (cfDNA) processing pipeline, Triton conducts fragmentomic and phased-nucleosome coverage analyses on individual or composite genomic regions and outputs both region-level biomarkers and nt-resolution signal profiles.

Converts the string output of BPROM, a promoter prediction software tool, to the GFF3 file format. Used in a CPT Galaxy phage genomics workflow

Comprehensive in silico genomic analysis pipeline for domesticating non-model bacteria (Core module)

Touché: scalable enhancer–promoter contact analysis for Micro-C and Hi-C data

miRNA promoter annotation based on deepCAGE data

This tool allows you to send predefined messages to target Instagram users. It sends your message to the targets every 3 minutes. You can use this tool to advertise your products to your potential customers. Just start the bot and lay down!

Fine-tuning and interpreting the HyenaDNA genomic language model on DNA-structure tasks (Z-DNA, G-quadruplexes, promoters) using Explainable-AI attribution methods.

More accessible dump of the PWMs from ElemeNT (10.1080/21541264.2015.1067286)

R package for promoter region extraction and annotation from GTF files.

Best site you have ever seen ✨

Interactive web viewer for TF ChIP-seq binding programs at canonical protein-coding TSSs (Ensembl GRCh38.114). Streamlit + Plotly + DuckDB; ~1,300 TFs × ~19,700 TSSs; NMF programs/archetypes, GTEx + DepMap overlays, atlas-wide TF×TF network.

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