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

TFregulomeR reveals transcription factors’ context-specific features and functions

Python script to quickly extract promoter and terminator regions with the NCBI API. Search for the presence of individual pattern or transcription factor responsive elements with manual sequence (IUPAC) or JASPAR API.

TFregulomeR reveals transcription factors’ context-specific features and functions

DNA Motif discovery that includes the discovery of flexible (long or gapped) motifs.

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

TFregulomeR reveals transcription factors’ context-specific features and functions

Anchor Residue Identification for any TF

Plot position weight matrices (PWM)

Deep Unfolded Convolutional Dictionary Learning for motif discovery.

Published in GigaScience. Web app for post-GWAS/QTL analysis that performs a slew of novel bioinformatics analyses to cross-reference GWAS/QTL mapping results with a host of publicly available rice databases

Which ESR1 and PGR binding sites are functional?

Prediction of the binding sites of multiple transcription factors in a whole genome

Automated analysis tool for mutations in promoters, transcription factor binding sites, coding regions and protein domains in the context of gene regulatory networks.