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
RSCU_RS: Measuring the bias in…
Overview Overview: In the protein coding sequences of a species, the 61 possible codons of the genetic code are not equally distributed. This observation is referred to as the Codon Usage Bias (CUB) of a species. Several measures have been proposed to quantify the CUB using the frequencies of codons in all RNA coding sequences…
FastME 2.0
FastME is a software package for the fast and accurate inference of phylogenetic trees from distance matrices. It implements algorithms based on the Balanced Minimum Evolution (BME) principle, a distance-based criterion closely related to the Neighbor Joining (NJ) method. The goal of the BME framework is to identify the phylogenetic tree that minimizes the total…
MYST
What is MYST? MYST 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…