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Multiple Sequence Alignment and Phylogenetic Analysis

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16 views17 pages

Multiple Sequence Alignment and Phylogenetic Analysis

Uploaded by

chongocletus02
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Multiple Sequence Alignment and

Phylogenetic analysis

6/2/2024 -SP- 1
Sequence alignment
• Sequence alignment is the procedure of comparing two or more
nucleotide or amino acid sequences to identify regions of similarity
between the sequences.

• Sequence alignment could be pair-wise alignment when


comparing two sequences or multiple sequence alignment (MSA)
when comparing more than two sequences.
• Softwares for Sequence alignment include Muscle, ClustalW,
MAFFT etc.

6/2/2024 -SP- 2
Local and Global alignment
• Global alignment is a method of comparing two sequences,
which aligns the entire length of the sequences by
maximizing the overall similarity.

• In local alignment, instead of attempting to align the entire


length of the sequences, only the regions with the highest
density of matches are aligned.

6/2/2024 -SP- 3
Importance of sequence alignment
1. helpful in prediction/understanding the functional of
function
2. helpful in understanding sequence divergence or
evolutionary relationships between the sequences.
3. Useful sequence assembly
4. database searching
5. gene finding
6. Useful in mutation calling
7. MSA is also a prerequisite for constructing phylogenetic
trees
6/2/2024 -SP- 4
Multiple Sequence Alignment
perform MSA on the following sequences
1. GAAATTCTACCAGTGTCTATGACCAAGA
2. GAAATTCTACCAGAGTCTATGTCCAAGA
3. GAAATTCTACCAGTGTCTATCACCAAGA
4. GAAATTCTACCAGTGTCTATGACCAA
5. GAAATTCTACCAGTGTCTATGACCAAGA
6. GAAATTCTACCAGTGTCTATGACCAAGG
7. GAATTCTACCAGTGTCTATGACCAAGA

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Multiple Sequence Alignment
1. GAAATTCTACCAGTGTCTATGACCAAGA If sequence 1, is the
2. GAAATTCTACCAGAGTCTATGTCCAAGA reference sequence, then
3. GAAATTCTACCAGTGTCTATCACCAAGA there are mutations
-in sequence 2 where T is
4. GAAATTCTACCAGTGTCTATGACCAA- -
substituted with A,
5. GAAATTCTACCAGTGTCTATGACCAAGA -in sequence 3 where G is
6. GAAATTCTACCAGTGTCTATGACCAAGG substituted with C
7. GA- ATTCTACCAGTGTCTATGACCAAGA -in sequence 6 where A is
substituted with G

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6/2/2024 Multiple sequence alignment -SP- 7
Phylogenetics
• A phylogenetic tree is an estimate of the relationships among
taxa (or sequences) and their hypothetical common
ancestors.
• It’s the study of evolutionary relationships.
• Phylogenetic analysis is a means of inferring or estimating
these relationships.
• Two species are more related if they have a more recent
common ancestor, and less related if they have a less recent
common ancestor

6/2/2024 -SP- 8
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Characteristics of a phylogenetic tree
Basic characteristics of a phylogetic tree include:
 Node is the branch point in the tree
 branch represents the descendant and ancestry
 a clade is a group of organisms that include all descendants of a
common ancestor
 the root is the common ancestor between the clades.
 branch length corresponds to changes in the branches

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phylogenetic tree

Presentation of the elements


of a phylogenetic tree

In phylogenetics members of a group/clade share a common


evolutionary history and are more related to each other than
members of another group.
6/2/2024 -SP- 11
importance of phylogenetic analysis
 Identifying unknown species: phylogenetic analysis can aid in
the discovery and classification of new species.
 Understanding evolutionary relationships:
Tracing disease outbreaks: Phylogenetic analysis of pathogens
like viruses and bacteria helps track the origin and spread of
diseases, informing public health responses.
Used in classification and naming of organisms
inferring the functions of genes that have not been studied
experimentally, and elucidating mechanisms that lead to
microbial outbreaks among many others.
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Steps in phylogenetic analysis
• Building a phylogenetic tree requires four distinct
steps:
Step 1- identify and acquire a set of homologous DNA or
protein sequences
Step 2- Multiple sequence alignment (MSA)
Step 3- Determination of substitution model
Step 4- Tree re-construction.

6/2/2024 -SP- 13
Softwares for phylogenetic tree construction
• MEGA (Molecular Evolutionary Genetics Analysis)
• MrBayes
• PHYLIP
• BEAST
And many others

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Methods for estimating phylogenetic trees
They can be classified into 2:
1.Distance based methods
-Neighbour-Joining (NJ)
-Unweighted Pair Group Method with Arithmetic mean
(UPGMA)
2. Character based methods
-Maximum Parsimony
-Maximum Likelihood
-Bayesian analysis
6/2/2024 -SP- 15
Rooting a tree
Trees may be rooted or unrooted
• Roots allow the determination of the direction of descent from a
common ancestor
• Outgroups are used to determine where the root should be placed on
the tree
• Appropriate out groups must be selected and included in the
alignment

6/2/2024 -SP- 16
Practical 2.
Title : Multiple Sequence Alignment and Phylogenetic
construction.

You will be provided with the necessary software,sequences and


walked through the entire procedure.

6/2/2024 -SP- 17

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