Namra-5/HBB-Gene-Genomics-Analysis-Pipeline

Six-task genomics analysis of the HBB gene using seven African population sequences. NUST SINES Bioinformatics Project 2026. # HBB Gene Genomics Analysis Pipeline **Genomics Pre-Midterm Project | BS Bioinformatics UG-1** School of Interdisciplinary Engineering and Sciences (SINES) National University of Sciences and Technology (NUST), Islamabad | Field | Detail | |-------|--------| | Authors | Namra Basharat, Ghania Munir, Hania Fahad, Nawal Babar | | Roll Numbers | 476203, 460673, 455132, 459508 | | Gene | HBB — Hemoglobin Subunit Beta (Gene ID: 3043) | | Organism | *Homo sapiens* | | Reference | NC_000011.10 (GRCh38.p14, chr11:5,225,464–5,227,071) | | Date | March 2026 | --- ## Project Overview This repository contains the complete data, output files, and analysis scripts for a six-task genomics pipeline applied to the human **HBB (Hemoglobin Subunit Beta)** gene. The HBB gene was selected because a single point mutation at codon 6 (Glu6Val, rs334) causes Sickle Cell Disease (SCD), one of the most prevalent inherited disorders worldwide, with the highest burden in sub-Saharan Africa. Seven sequences were analyzed: one GRCh38 reference sequence and six population-level voucher sequences from African populations in Cameroon, Nigeria, Gabon, Uganda, and Senegal. The analysis covers data retrieval, genome visualization, pairwise and multiple sequence alignment, repeat element identification, variant calling and annotation, gene structure prediction, and orthology inference. --- ## Dataset | No. | Accession | Population | Country | Length | |-----|-----------|-----------|---------|--------| | 1 | NC_000011.10 | GRCh38 Reference | — | 1,608 bp | | 2 | MK476281.1 | Nzime | Cameroon | 1,824 bp | | 3 | MK475906.1 | Bakoya | Cameroon | 1,824 bp | | 4 | MK476491.1 | Yoruba | Nigeria | 1,824 bp | | 5 | MK476080.1 | Bakota | Gabon | 1,824 bp | | 6 | MK476374.1 | Kiga | Uganda | 1,824 bp | | 7 | MK476446.1 | Mandenka | Senegal | 1,824 bp | All sequences retrieved from NCBI Nucleotide and validated by BLASTN (100% identity, 100% query coverage, E-value = 0.0). --- ## Analysis Pipeline ``` …