Affiliation:
1. Université Côte d'Azur
Abstract
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.
Publisher
Research Square Platform LLC
Reference18 articles.
1. Evaluating tools for transcription factor binding site prediction;Jayaram N;BMC Bioinf déc,2016
2. Castro-Mondragon JA, Riudavets-Puig R, Rauluseviciute I, Berhanu Lemma R, Turchi L, Blanc-Mathieu R et al. JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. Nucleic Acids Research. 7 janv. 2022;50(D1):D165–73.
3. TRANSFAC(R) and its module TRANSCompel(R): transcriptional gene regulation in eukaryotes;Matys V;Nucleic Acids Research 1 janv,2006
4. Identification of patterns in biological sequences at the ALGGEN server: PROMO and MALGEN;Farre D;Nucleic Acids Research 1 juill,2003
5. Estimating transcription factor bindability on DNA;Tsunoda T;Bioinf 1 juill,1999