Work

TFinder: A Python Web Tool for Predicting Transcription Factor Binding Sites

Year: 2024

Type: article

Abstract: Background: Transcription is a key cell process that consists in synthesizing several copies of RNA from a gene DNA sequence. This process is highly regulated and closely linked to the ability of transcription factors to bind specifically to DNA. TFinder is an easy-to-use Python web portal allowing the identification of Individual Motifs (IM) such as Transcription Factor Binding Sites (TFBS). Results: Using the NCBI API, TFinder extracts either promoter or gene terminal regulatory regions, through a simple query of NCBI gene name or ID. It enables simultaneous analysis across five different species for an unlimited number of genes. TFinder searches for Individual Motifs in different formats, including IUPAC codes and JASPAR entries. Moreover, TFinder also allows de novo generation of a Position Weight Matrix (PWM) and the use of already established PWM. Finally, the data are provided in a tabular and a graph format showing the relevance and the P-value of the Individual Motifs found as well as their location relative to the Transcription Start Site (TSS) or the terminal region of the gene. The results are then sent by email to users facilitating the subsequent data analysis and sharing. Conclusion: TFinder is written in Python and freely available on GitHub under the MIT license: https://github.com/Jumitti/TFinder. It can be accessed as a web application implemented in Streamlit at https://tfinder-ipmc.streamlit.app. Resources are available on Streamlit “Resources” tab. TFINDER strenght is that it relies in an all in one intuitive tool allowing users inexperienced with bioinformatics tools to retrieve gene regulatory regions sequences in multiple species and to search for individual motifs in huge number of genes.

Source: Journal of Molecular Biology

DOI: 10.1016/j.jmb.2024.168921

Authors: Julien Minniti, Frédéric Checler, Eric Duplan, Cristine Alves da Costa

Institutions: Centre National de la Recherche Scientifique, Inserm, Institut de Pharmacologie Moléculaire et Cellulaire, LabEx DISTALZ

Language: English

Topic: Genomics and Chromatin Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: hybrid

Estimated APC paid: $4,420

Funder: Agence Nationale de la Recherche