A Comprehensive Sequence Analysis of the Human TNF Gene

This is a repository for the comprehensive sequence analysis of the human tumor necrosis factor (TNF) gene, focusing on variant detection, functional annotation, gene study insights and key findings.

Objective:

To analyze and interpret the human TNF gene sequence, which encodes a proinflammatory cytokine called TNF.

Project Tasks and Workflow:

1. Downloading the human TNF gene sequence.
2. Translating the sequence into amino acids.
3. Finding open reading frames (ORFs) within the sequence.
4. Analyzing the sequence composition.
5. Identifying transcription factor binding sites (TFBS).
6. Searching for functional motifs within the sequence.
7. Predicting the coding and non-coding regions within the sequence.
8. Converting the sequence from FASTA to PHYLIP format.

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.