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Assignment#3 Bioinformatics

This document presents an analysis of the H-NOX gene using the NCBI Gene Database and BLAST to identify similarities with other genes. The findings reveal a high conservation of the H-NOX gene among Caulobacter species, with 100% sequence identity, while showing lower similarity with Massilia species. The study emphasizes the gene's evolutionary significance and the utility of bioinformatics tools in gene analysis.

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1 views5 pages

Assignment#3 Bioinformatics

This document presents an analysis of the H-NOX gene using the NCBI Gene Database and BLAST to identify similarities with other genes. The findings reveal a high conservation of the H-NOX gene among Caulobacter species, with 100% sequence identity, while showing lower similarity with Massilia species. The study emphasizes the gene's evolutionary significance and the utility of bioinformatics tools in gene analysis.

Uploaded by

attasaiffaseeh456
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© © All Rights Reserved
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Assignment#3 H-NOX Gene Analysis Using BLAST

Done by
Saif ur Rehman (FA24-BCS-044)
Abdullah Faisal Butt (FA24-BCS-006)
Muhammad Usman (FA24-BCS-048)
Anas Khalid (FA24-BCS-018)
Yousuf Samiullah (FA24-BCS-122)

Date: 25th March,2025.

Objective:
The objective of this study is to analyze the H-NOX gene using the NCBI Gene Database and
BLAST (Basic Local Alignment Search Tool) to identify its similarities with other genes. The
report aims to document the process of retrieving the gene sequence, performing a BLAST
search, and interpreting the results to understand its potential biological significance.
H-NOX Gene
The H-NOX (Heme-Nitric Oxide/Oxygen binding) gene is found in both bacteria and animals,
where it helps cells detect and respond to nitric oxide (NO), an important signaling molecule. In
bacteria, it plays a role in communication and biofilm formation, while in animals, it helps
regulate blood vessel relaxation. By studying the H-NOX gene using tools like NCBI and BLAST,
researchers can compare its sequence with other genes to understand its function and
importance.

Tools used:
NCBI Gene Database: https://www.ncbi.nlm.nih.gov/gene
BLAST Tool: https://blast.ncbi.nlm.nih.gov/Blast.cgi

Procedure
1. Finding the H-NOX Gene From NCBI
1. Open NCBI Database in browser.
2. Shortlist the database to gene and search for H-NOX gene.
3. 3.Click on the first option to open complete detail of H-NOX gene.
2. Open FASTA Sequence
1. Scroll down and click on FASTA option situated in right side with Genbank and Graphics
option.
2. This will give FASTA sequence.

3. Run Blast
1. Click on the Run Blast option.
2. This will directly open the BLAST tool with the sequence preloaded.
3. Verify that the correct BLAST program is selected (e.g., BLASTn for DNA or BLASTp for
proteins).
4. Click "BLAST" to start the analysis.
5. Wait for the results, then review the sequence alignments, similarities, and matching
organism.
Findings
The BLAST analysis of the H-NOX gene sequence revealed significant similarities with various
bacterial species, particularly within the Caulobacter genus. The results indicate a high level of
conservation of this gene among closely related species, with some variations observed in other
bacterial strains. The key findings from the analysis are as follows:
1. High Similarity with Caulobacter Species:
o The H-NOX gene exhibits 100% sequence identity with Caulobacter vibroides
strains CB1, CB S2B, NA1000, and CB15.
o This suggests that the gene is highly conserved within this genus, indicating its
essential functional role in these bacteria.
2. Minor Variations in Some Strains:
o The gene sequence in Caulobacter vibroides CB2A and CB2 shows 98.75%
identity, indicating slight mutations.
o These differences may represent evolutionary adaptations within the species.
3. Lower Similarity with Massilia Species:
o The alignment with Massilia sp. WG5 shows 81.33% identity, significantly lower
than the Caulobacter strains.
o This suggests that while the gene exists in Massilia, it has undergone
considerable evolutionary changes.
4. Significance of E-Values:
o The E-values for top Caulobacter matches are 0.0, confirming the reliability of
these alignments.
o The Massilia strain has an E-value of 3e-04, indicating a weaker but still notable
relationship.
These findings highlight the evolutionary conservation of H-NOX in Caulobacter species and its
divergence in more distantly related bacteria.
Conclusion
The BLAST analysis of the H-NOX gene showed high similarity with Caulobacter vibrioides
strains, with 100% identity, indicating strong conservation. A lower similarity (81.33%) with
Massilia sp. WG5 suggests evolutionary differences. Additional insights can be gained from the
Alignments, Taxonomy, and Graphic Summary sections, which provide sequence comparisons,
evolutionary links, and visual data.

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