BioinformHER Mini-Project: Comprehensive sequence analysis of the human TNF gene:

This is a repository for the BioinformHER Module 1 Mini Project, containing sequence files, analysis report, gene study insights and key findings.

Objectif:

In this project, I conducted an in-depth sequence analysis of the Human Tumor Necrosis Factor (TNF) gene, employing a range of bioinformatics tools including BioEdit, GENSCAN, PROMO, and more in order to explore the structural and functional characteristics of the Human TNF (tumor necrosis factor) gene.

Tools used:

1. NCBI (database): a comprehensive resource/ database that provides access to sequence data, information and tools related to bioinformatics.
2. BioEdit: is a biological sequence alignment editor that is widely used for sequence alignment, editing, ORF finding, analysis and visualization of DNA, RNA and protein sequences.
3. PROMO: is a web-based tool used to identify/ predict TFBS within the DNA sequence, which is useful in understanding gene regulation mechanisms.
4. MEME Suite: Multiple EM for Motif Elicitation (MEME) is a core tool in the suite, useful for identifying and visualizing functional motifs in biological sequences.
5. GENSCAN: is a computational tool used for predicting coding (exons) and non-coding (introns) regions in a DNA sequence.

Project Tasks and Workflow:

1. Downloading the human TNF gene sequence from NCBI database
2. Translating the sequence into amino acids using Bioedit in order to understand the functional role of the gene's coding potential.
3. Identifying open reading frames (ORFs) within the sequence and predict the protein-coding regions
4. Analyzing the sequence composition.
5. Identifying transcription factor binding sites (TFBS) to understand regulatory mechanisms affecting gene expression.
6. Searching for functional motifs within the sequence using MEME.
7. Predicting the coding and non-coding regions within the sequence.
8. Converting the sequence from FASTA to PHYLIP format.