Experiment 1

Aim: Phylogenetic tree analysis for gene and protein.

Theory: Phylogenetic tree is diagram of branching pattern which shows the link between different
organisms. It shows branching of various organisms which are evolved from a common ancestor
which are the nodes in the tree.

The roots define the ancestral line and as you move towards the branching the connecting line to
the main branch gives the time.

Types of phylogenetic trees:

Unscaled branches – Cladogram / cladistic trees

Scaled branches – Phylograms

Newicks representation

A phylogenetic tree is built using

. morphological

. biochemical

. behavioural

. molecular features of species or other groups

Phylogeny tree building methods:

1) Distance methods: based on sequence similarities.

Ex- VPGMA, Neighbouring joining
Drawbacks: additive distance error
2) Maximum Likelihood
Drawbacks: computationally complex
will result in multiple trees.

Bootstrapping: Measures the confidence of the phylogenetic tree.

Bootstrap value: >90% - strongly supported

70 >90% - supported

50 >70% - weakly supported

<50% - not supported

Why we studying phylogenetics trees which explains the phylogenetic relationships?

- To understand the evolution that has happened

- If evolution is understood then we can also reach out for molecular level and understanding
at molecular level will help to create many things artificially even life forms.
- We can get solution to survive natural disasters.

Requirements: Laptop with internet connection

Protocol:
- NCBI page was opened and the search bar was categorized to homologene.

- gene for the insulin was typed, that is INS.

-A page opened up, then proceeded to choose the option which is required to be downloaded. Gene
and protein sequences were downloaded and named them accordingly. Also the texts sequences
were edited, only the name was kept and rest other information were omitted as this would result in
a much spacious tree formation and not crowded by a long line of information besides its branch.

-Open BLASTN and BLASTP so as to BLAST (Basic Local Alignment Search Tool) the gene and protein
respectively. By doing blast it would obtain a phylogenetic tree based on evolutionary relation
between all the chosen sequences by inferring the members of its family and would display its
respective phylogenetic tree.

-The phylogenetic tree obtained were changed to slanted form for better observation.

- Then gene and protein sequence for haemoglobin gene, mitochondrial gene and cytochrome c
were downloaded and edited.

Result:
Phylogenetic trees:

-INS Gene - INS protein

-Haemoglobin Gene (HBD) -Haemoglobin protein (HBD)

-Mitochondrial gene (MT-CO1)

-Mitochondrial protein (MT-CO1)

-Cytochrome C Gene (CYT-C) -Cytochrome C protein (CYT-C)

Discussion:
Name: Tapaswani Sethi

Roll No: 418LS5039