TFinder Official Launch

TFinder is now available 🧬🔍 -->

Overview

TFinder is a Python easy-to-use web tool for identifying Transcription Factor Binding Sites (TFBS). It allows easy extraction of either the promoter or terminal regions of a gene by simple inquiry of unique NCBI API keys. It allows the simultaneous analysis of five different species of an unlimited number of genes. The tool allows the search of TFBS in different formats, including IUPAC codes and JASPAR entries. Moreover, TFinder also allows the generation and use a Position Weight Matrix (PWM). Finally, the data may be recovered in a tabular form and a graph showing the relevance of the TFBSs as well as its location relative to the transcription start site (TSS) or gene end.

TFinder is written in Python and is freely available on GitHub under the MIT license: https://github.com/Jumitti/TFinder and can be accessed as a web application implemented in Streamlit at https://tfinder-ipmc.streamlit.app.

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Description

Transcription factors (TFs) are proteins that bind to DNA to regulate gene expression. They specifically recognize a nucleotide sequence called a transcription factor binding site (TFBS) in the promoter and terminator regions of genes. The search of these TFBSs is an empirical discipline in the field of genomics that concerns a key step before TFBS functional validation by gel shift assays (EMSA) and chromatin immunoprecipitation (ChIP) that allow the examination of the interaction between a TF and DNA (Jayaram, Usvyat and R. Martin 2016)

The in-silico research of TFBS can be tedious and time-consuming at various stages, especially for novices in the discipline. Thus, first, it is necessary to retrieve the promoter or terminator nucleotide sequence of a gene. This step may be achieved by the utilization of several databases such as NCBI, UCSC and Ensembl, but they are not intuitive and user-friendly. Next, after identifying the promoter sequence of interest, one may use TF databases such as JASPAR (Castro-Mondragon et al. 2022) and TRANSFAC (Matys 2006), but they have their limitations. For example, these platforms do not allow the search of TFBS from an unreferenced TF and may be subject to a fee. Other tools such as PROMO (Farre 2003), TFBIND (Tsunoda and Takagi 1999), TFsitescan make it possible to find all the TFs binding to a nucleotide sequence; nevertheless, they all use JASPAR and TRANSFAC databases and do not allow use of personal TF and their TFBS. Moreover, these tools are rather archaic and not very user-friendly. There is only MEME that allows research with of your “own” TFBS (Bailey et al. 2015). MEME has a large tool library but is a niche software suite. FIMO is their most similar tool to TFinder (Grant, Bailey and Noble 2011).

TFinder is an ultra-intuitive, easy-to-use and fast analysis open source and free tool that allows both the retrieval and search of TFBS in a unique site. TFinder allows the analysis of an unlimited number of genes; the selection of up to five different species (human, mouse, rat, drosophila, zebrafish); the choice and examination of either promoter or terminator gene regions; the configuration of an upstream downstream window of sequence analysis and the search of TFBS in different formats including IUPAC code, a JASPAR ID or a Position Weight Matrix. TFinder, searches for TFBS on the sense and antisense strand but also considers the search with the complementary forms. The software takes care of everything in record time.

Browser compatibility

• Opera GX
• Chrome (also Chromium)
• Safari
• Edge
• Mozilla

Functions

Promoter/Terminator Extractor

• Extract mutliple promoter/terminaotr regions using ENTREZ_GENE_ID or NCBI Gene NAme in FASTA format with NCBI API

• Species: Human 🙋🏼‍♂️, Mouse 🖱, Rat 🐀, Drosophila 🦟, Zebrafish 🐟

• Set Upstream and Downstream from Transcription Start Site (TSS) and Gene End

• Mode "Advance": allows to extract for the same gene the promoter and terminator regions for several species

Binding Site Finder

• Support multiple promoter/terminator regions in FASTA format
• Find transcription factor responsive elements
• Support IUPAC code for responsive elements
• Support PWM transcription factor with JASPAR API
• Generate PWM for personnal responsive elements
• Calculation of the distance of the found sequence to TSS or Gene End
• Relative Score calculation: (score element found - minimum score matrix reference)/(score maximum matrix reference- minimum score matrix reference)
• p-value: 1000000 random sequences of reactive element length are generated based on the proportion of A, T, G, C in the search sequence. p-value=(Nb Rel Score random sequences >= Rel Score of elements founds)/ (Nb random seq generated). p-value is the number of random sequences generated having a relative score greater than or equal to the relative score of the element found divided by the number of random sequences generated
• Export results to excel (.xlsx)
• Export results, sequences, parameters via e-mail
• Graph of sequence positions found on the promoter

More

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Credit & Licence & Citation

Copyright (c) 2023 Minniti Julien.

This software is distributed under an MIT licence. Please consult the LICENSE file for more details.

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