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Computational Genomics

The document outlines a computational genomics task involving the comparison of beta-globin genes from humans and mice using dot plots and sequence alignment tools. It also details the alignment of hemoglobin sequences and mitochondrial COI genes from multiple species, culminating in the construction of a Neighbour-Joining tree to illustrate phylogenetic relationships. Key findings include the close relationship between humans and monkeys, and elephants and rats, with a high confidence level indicated in the tree structure.

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sama ghorab
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11 views18 pages

Computational Genomics

The document outlines a computational genomics task involving the comparison of beta-globin genes from humans and mice using dot plots and sequence alignment tools. It also details the alignment of hemoglobin sequences and mitochondrial COI genes from multiple species, culminating in the construction of a Neighbour-Joining tree to illustrate phylogenetic relationships. Key findings include the close relationship between humans and monkeys, and elephants and rats, with a high confidence level indicated in the tree structure.

Uploaded by

sama ghorab
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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Task 1

Computational Genomics

Team :
Rahma Ezzat Mohamed
Samaa Gorab
Shahd Mohamed

Dr. Mohammed El-Ghannam


Dr. Salma Magdy
1. A fragment of the human beta-globin gene vs. the mouse beta-globin gene.

○​ Use an online dot plot tool to identify regions of similarity.


○​ Adjust the window size and threshold to see how it affects
sensitivity.
a.​ Open NCBI to get sequence of human beta-globin gene , mouse beta-globin
gene
-​ human beta-globin gene
-​ Choose Nucleotide and then choose the first result
-​ Choose CDS and choose FASTA

And copy the sequence to past in DOTLET


-​ mouse beta-globin gene
** Now we have two seq of human beta-globin gene , mouse beta-globin gene

b.​ Open Dotlet Js to make Alignment

Insert SEQ 1 and SEQ 2

Choose the best window size is 40 and scoring matrix is BLOSUM 62


Choose the best threshold is 50%

The Final Result :

Parallel Lines on Either sites of the main diagonal => Direct Repeat
2. Download hemoglobin sequences (human vs. mouse) from NCBI.

· Align globally, calculate % identity, and annotate conserved regions.

· To align globally we use the site: https://www.ebi.ac.uk/jdispatcher/psa

→ Needleman --> global alignment (must be the same length)

→ We click on EMPOSS Needle

· We must paste here the hemoglobin protein sequences for human and
mouse, so we will get them from NCBI:
●​ Copy the FASTA sequence from second line and paste it in the
website

●​ And the same thing for mouse sequence and click submit then
view results
· Here is the global alignment result:
· most positions are matched (|), and some have similar but not
identical residues (: or .)
3. Mitochondrial COI gene from 3 species: Human, Elephant, Rat, Monkey

· Download sequences from NCBI in FASTA format.

· Align using ClustalW in MEGA (default settings).

· Build an NJ tree with.

· Download sequences from NCBI in FASTA format.


· Align using ClustalW in MEGA (default settings).
All the downloaded files in fasta format then collects them in one txt file and convert
it to fasta format

Open the a session in mega and choose the fasta file with collected sequence
Making Multiple sequence alignment with ClustalW and choosing the default
parameters

The result of the alignment


Save the alignment result at Mitochondrial COI gene.mas file

Save the output file in .mega file to be able to make ‘Compute Amino Acid
Composition’ and ‘Constructing Neighbour-Joining Tree’
(Bonus) Compute Amino Acid Composition
After using the mega data in the session we translate the nucleotide sequense to
convert it to amino acids

The highest amino acid in composition is Leucine in Rat


· Build an NJ tree with.

Putting the same parameters as the file but the substitution type here is amino acid

Phylogenatic Tree result


The species compared here are: Homo (humans), Monkey, Elephant, and Rat.​
The tree structure shows how closely related these species are:

●​ Homo (human) is most closely related to the Monkey, as they branch from a
common ancestor.
●​ Elephant is is most closely related to the Rat, as they branch from a common
ancestor.
○​ This number (98) indicates high confidence (98%) in that particular
branch of the tree (it's based on bootstrapping, a statistical method).

The scale bar (0.01) represents genetic distance — how much change has occurred.
Smaller values mean closer relationships.

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