TFscope
Characterizing the binding preferences of transcription factors (TFs) in different cell types and conditions is key to understand how they orchestrate gene expression. TFscope is a machine learning approach that identifies sequence features explaining the binding differences observed between two ChIP-seq experiments targeting either the same TF in two conditions or two TFs with similar motifs (paralogous TFs). TFscope systematically investigates differences in the core motif, nucleotide environment and co-factor motifs, and provides the contribution of each key feature in the two experiments.
TFscope online execution
Other tools
DExTER
Overview DExTER (Domain Exploration To Explain gene Regulation) is a bioinformatics tool designed to automatically identify genomic regions whose nucleotide composition correlates with gene expression levels. Unlike traditional approaches focusing on short transcription factor binding sites (6-12 bp), DExTER detects Long Regulatory Elements (LREs) that can span tens to hundreds of nucleotides. This makes it…
PhyML 3.0
Overview: new algorithms, methods and utilities PhyML is a software package that uses modern statistical approaches to build phylogenetic trees from the analysis of alignments of nucleotide or amino acid sequences. The main tool in this package builds phylogenies under the maximum likelihood criterion. It implements a large number of substitution models coupled to efficient…
TIDE
What is TIDE? TIDE is the orchestration platform behind ATGC online bioinformatics services. It provides a unified web interface and a public REST API to submit analyses, monitor jobs, and retrieve results across a growing catalog of phylogenetic and sequence-analysis tools. TIDE is a modernized redesign of WAVES, an older tool previously developped by ATGC…