Bioinformatics Analysis: Mutant cDNA Sequence and Protein Impact

This bioinformatics assignment focuses on analyzing a mutant cDNA sequence to determine its origin, the protein it codes for, and the impact of the mutation on protein function. The analysis involves aligning mutant and wild-type cDNA sequences to identify nucleotide differences and deduce the resulting amino acid substitution. The study also identifies the most closely related human protein homolog and examines the evolutionary conservation of NADH dehydrogenase subunit 3 across various species, culminating in the construction of a phylogenetic tree to assess evolutionary relationships. Discrepancies between expected and obtained protein sequences are discussed in the context of potential mutations and protein folding issues. The assignment leverages bioinformatics tools and databases to provide insights into the functional and evolutionary implications of the mutant cDNA sequence.

Running head: BIOINFORMATICS ASSIGNMENT 1
Bioinformatics assignment
Name of student
Name of institution

Running head: BIOINFORMATICS ASSIGNMENT 2
Bioinformatics assignment
The DNA sequence is a mutant cDNA sequence derived from an organism that displays an altered
phenotype to wild type organisms.
Using appropriate bioinformatics software and databases determine the following.
(1) What species is the wild type sequence derived from (give Linnaean and common species
names)?
Common name- Night monkey
Linnaean name- Aotus nancymaae
(2) . What protein does the wild type sequence code for?
Vitamin K epoxide reductase complex
(3) Align the mutant and wild type cDNA and answer the following questions.
a. How do the mutant and wild type DNA sequences differ? The wild type differs from the
mutant in a nucleotide. There is a mutation in one of the codons. A change in the
codon sequence results in the wrong protein being translated.
b. What is the nucleotide position of the change in the mutant? 661
(4) Use appropriate software to deduce the protein sequence that the mutant cDNA encodes and
align it with the wild type. Answer the following questions.

Running head: BIOINFORMATICS ASSIGNMENT 3
a. What is the codon position of the change in the mutant sequence? 665
b. What amino acid substitution results from the mutation? Leucine
(5) Briefly comment on the effect you think the mutation might have on the protein function and
phenotype of the organism using the results obtained in part 4.
Limit your answer to less than 60 words.
A mutation affects the protein structure. A mutation in the gene, can result in a wrong protein
being coded for. The protein may not fold properly altering the function. A Protein has three

Running head: BIOINFORMATICS ASSIGNMENT 4
types of structure, primary, secondary and tertiary. The tertiary structure determines the
function of the protein. It can involve other components such as lipids and carbohydrates.
(6) Use appropriate bioinformatics resources to find the most closely related human protein
homolog of the wild type sequence.
(i) What is the name of this protein?
Vitamin K epoxide reductase complex (Min, Lee, & Yoon, 2017)
(ii) Show a Clustal alignment of the wild type protein sequence aligned with the human
protein sequence.

Running head: BIOINFORMATICS ASSIGNMENT 5
(iii) Use appropriate literature to find out the sub chromosomal location of the human gene
encoding this protein and how many exons it has.
It has 38 exons (Yan & Wu, 2016)
(7) Select 22 orthologs of NADH dehydrogenase subunit 3-protein sequence from an
evolutionary diverse cross section of animal species including human and align these using
Clustal. Show the Clustal alignment output obtained. Use appropriate journal literature to find
features and amino acids and highlight these in the alignment. Comment on the evolutionary
conservation of these.

Running head: BIOINFORMATICS ASSIGNMENT 6
Figure 2 showing the evolutionary tree.
The above figure shows
Evolution has resulted in mutations in several genes. Some genes have become more effective
over the years; others were not expressed but now are being expressed while other genes are not
being expressed at all. Through evolution natural selection occurred allowing only the beneficial
genes to be propagated to the next generation. However, the NADH dehydrogenase sub unit 3
sequences have not changed. Amino acids coding sequences do not change since an alteration
affects the protein structure and function (Schauer et al., 2015). A change in the su unit results
in a change in the entire gene. The gene will translate a different protein. The new protein will
be different from NADH dehydrogenase. This is why the protein sub unit has not changed. The
original function and shape of the product has been maintained even after evolution.
(8) Using the data obtained in part, (8) select an appropriate protein sequence as an out-group and
draw a phylogenetic tree. In less than 150 words, comment on whether the result obtained is
as expected.

Running head: BIOINFORMATICS ASSIGNMENT 7
The results of the protein sequence obtained were not as expected. This can be attributed to the
presence of mutations. As evolution occurred, there was mutation in some of the gene loci,
especially in the non-coding regions. The expected results on the other hand, did not factor in
any mutations in the gene loci. Non-specific mutations could have also occurred for example,
deletion, insertation and substitution. This affects the protein that is being sequenced. A
different protein is observed. Improper protein folding can also be another factor that affected
the results of the protein sequence that were obtained. During protein, folding is when the
protein obtains its function and becomes a glycoprotein, a lipoprotein, or just a regular protein.
IF a protein is not folded properly, the phylogenetic tree will not be able to detect it in advance

Running head: BIOINFORMATICS ASSIGNMENT 8
References
Li, W., Cowley, A., Uludag, M., Gur, T., McWilliam, H., Squizzato, S., ... & Lopez, R. (2015). The
EMBL-EBI bioinformatics web and programmatic tools framework. Nucleic acids
research, 43(W1), W580-W584.
Min, S., Lee, B., & Yoon, S. (2017). Deep learning in bioinformatics. Briefings in
bioinformatics, 18(5), 851-869.
Schauer, M., Kottek, T., Schönherr, M., Bhattacharya, A., Ibrahim, S. M., Hirose, M., ... & Kunz, M.
(2015). A mutation in the NADH-dehydrogenase subunit 2 suppresses fibroblast
aging. Oncotarget, 6(11), 8552.
Yan, S., & Wu, G. (2016). Analysis on evolutionary relationship of amylases from archaea, bacteria
and eukaryota. World Journal of Microbiology and Biotechnology, 32(2), 24.