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Jumitti/TFinder
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TFinder is a Python easy-to-use web tool for identifying Transcription Factor Binding Sites (TFBS) and Individual Motif (IM). Using the NCBI API, it can easily extract either the promoter or terminal regions of a gene through a simple query of NCBI gene name or ID. It enables simultaneous analysis across five different species for an unlimited number of genes. The tool searches for TFBS and IM in different formats, including IUPAC codes and JASPAR entries. Moreover, TFinder also allows the generation and use of a Position Weight Matrix (PWM). Finally, the data may be recovered in a tabular form and a graph showing the relevance of the TFBSs and IMs as well as its location relative to the Transcription Start Site (TSS) or gene end. The results may be sent by email to the user facilitating the ulterior analysis and data sharing.

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Use Cases Limitations Evidence Owner's Insight

TFinder is ideally suited for researchers and students in genomics and bioinformatics who are analyzing gene expression regulation through transcription factors (TFs). It simplifies the identification of TF Binding Sites (TFBS) and Individual Motifs (IM) across different species, making it a valuable tool for comparative genomics studies, gene expression regulation analysis, and the initial steps of functional validation of gene regulation.

Based on pre-print paper found here: https://www.researchsquare.com/article/rs-3782387/v1

While TFinder streamlines the process of identifying TFBS and IMs, its efficacy may be limited by the completeness and accuracy of the NCBI database and JASPAR entries. The tool's performance can also be influenced by the quality of the input gene names or IDs, and its reliance on these databases means that newly discovered or less characterized transcription factors might not be fully represented.

The utility of TFinder has been demonstrated through its ability to facilitate the search for TFBS with various formats, including IUPAC codes and JASPAR entries, across five different species. This has proven beneficial in accelerating the early stages of genomic research that would otherwise be tedious and time-consuming.

This application was not uploaded by the author, but through their publicly available Github repository.

MIT License

Copyright (c) 2023 Minniti Julien

Prototype

Warning: Not intended for clinical use. Assume outputs are unsafe and unvalidated. Use carefully.


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J Julien Minniti

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