clustal omega.pptx

CLUSTAL OMEGA
(MULTIPLE SEQUENCE ALIGNMENT)
AINDRILA MITRA
BBT4

Sequence alignment:
A sequence alignment is a way of arranging sequences of DNA , RNA or
protein to identify regions of similarity that may be consequence of
functional, structural or evolutionary relationships between the
sequence.
In sequence alignment-
• The known sequence is known as the reference sequence.
• The unknown sequence is known as the query sequence.
1

Sequence alignment
Pairwise sequence alignment Multiple Sequence alignment
2

Pairwise sequence alignment:
It is used to align two biological sequence only.
Methods of primary sequence alignment:
1.Dynamic Programming: It is a general algorithm for solving certain optimization
problem. This technique can be applied to produce-
> Global alignment (Needleman-Wunsch algorithm)
> Local alignment (Smith-Waterman algorithm)
2.Dot Matrix: It is a grid system where the similar nucleotides of two DNA
sequences are represented as dots.
3

Multiple sequence alignment:
Multiple sequence alignment (MSA) is generally the alignment of three
or more biological sequence of similar length.
MSAs are often used in identifying conserved sequence regions across
a group of sequences hypothesized to be evolutionarily related.
Alignments are also used to aid in establishing the evolutionary
relationship by constructing phylogenetic tree.
4

APPLICATION OF MSA:
• Detection of structural homologies.
• Detection of conserved domains.
• Construction of phylogenetic tree.
• Prediction of a protein structure.
• Determination of a consensus sequence.
5

Methods of MSA
Dynamic
programming
Progressive Method
Iterative method
Motif Finding
Hidden Markov
Model 6

Dynamic
Programming
Progressive
Method
Iterative
Method
Motif Finding Hidden
Markov
Model(HMM)
This is an extension
of dynamic
programming
approach for
pairwise alignment
to multiple
sequence. Because
of its high running
time it is not
typically used in
practice.
Progressive ,
hierarchical, or tree
methods generate a
multiple sequence
alignment by first
aligning the most
similar sequence
and then adding
successively less
related sequences
or groups to the
alignment until the
entire query set has
been incorporated
into the solutions
It is a method of
performing a series
of steps to produce
successively better
approximation to
align many
sequence step-by-
step. Here the
pairwise sequence
alignment is totally
avoided.
It is also known as
profile analysis,
constructs global
multiple sequence
alignments that
attempt to align
short conserved
sequence in the
query set.
Hidden Markov
model have been
used to produce
probability scores
for a family of
possible multiple
sequence
alignments for a
given query set.
7

Clustal W
Clustal Omega
T-coffee (Tree based Consistency Objective function for
alignment Evaluation)
MUSCLE (Multiple Sequence Comparison by Log-Expectation)
DIALIGN 2
MSA TOOLS
8

https://www.researchgate.net/publication/275954941_Multiple_Sequence_Alignment_Tools_Assessing_Performance_of_the_Underlying_Algorithms
LIST OF MSA TOOLS:
9

CLUSTAL OMEGA: (https://www.ebi.ac.uk/Tools/msa/clustalo/)
The Clustal series of programs are widely used in molecular biology for
the multiple alignment of both nucleic acid and protein sequences and
for preparing phylogenetic tree.
Example: Clustal V, Clustal W, Clustal X, Clustal omega, Clustal2
Clustal omega has the widest variety of operating systems out of all the
clustal tools.
10

Clustal omega uses seeded guide tree and HMM profile-profile
techniques to generate alignment.
Clustal omega follows 5 main steps:
1. The first is producing a pairwise alignment using the k-tuple
method, also known as the word method.
2. After that the sequence are clustered using the modified mBed
method.
3. It is followed by the k- means clustering method.
4. Guide tree is constructed using UPGMA algorithm.
5. In the final step, the multiple sequence alignment is produced using
HHAlign package from the HH-Suite which uses two profile HMM.
Fig: Flowchart of algorithms used
in clustal omega
(https://en.wikipedia.org/wiki/Clustal#/media/File:Clustal_O
mega_Algorithm_Flowchart.svg
)
11

STEPS :
• Step1: go to NCBI> select gene>search
12

Step2: select Homo sapiens> redirect to new page
13

Step3: select genbank> new page>scroll down> cds> protein id>click
14

Step5: select organism based on
percentage identity> download
the FASTA (aligned sequence)
17

Step6: go to Clustal omega> paste the sequence>submit
18

Conservative
mutation(:)
Conserved
sequence (*)
Gap(-)
Semi
conservative
mutation(.)
19
Interpretation of the Sequence alignment:

Conserved sequence(*): the amino acid is the same for all sequences
at that position.
Conservative substitution(:) : The replacement of an amino acid
residue in one protein by one with similar chemical properties in
another protein .
Non-conservative substitution(): The replacement of an amino acid
residue in one protein by one with dissimilar chemical properties in
another protein.
Semi-conservative substitution(.): which is somewhere between a
conservative and nonconservative substitution. This means that the
chemical properties of the amino acids at that position are similar,
but not that similar.
20

Different colours represents different amino acid residues according to
their physicochemical properties.
https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/Clustal+Omega+FAQ
21

Phylogenetic tree is a
branching diagram
showing the evolutionary
relationships among the
given sequences.
Cladogram is a type of
phylogenetic tree which
only represent the
branching pattern.
22

Conclusion:
Clustal omega uses a modified iterative progressive
alignment method and can align over 10,000 sequences
quickly and accurately.
It is very useful for finding evidence of conserved function in
DNA and protein sequences.
23

REFERENCE:
• https://www.researchgate.net/publication/10693451_Multiple_sequence_alignment_with_t
he_CLUSTAL_series_of_programs
• https://pubmed.ncbi.nlm.nih.gov/33289883/
• https://en.wikipedia.org/wiki/Clustal
• https://www.slideshare.net/ShumailaRiaz6/multiple-alignment-sequence-using-clustal-
omega-shumaila-riaz
• https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/Clustal+Omega+FAQ
• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9024764/
• https://www.slideshare.net/MariyaRaju/multiple-sequence-alignment-76802660
• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5734385/
• https://www.researchgate.net/publication/275954941_Multiple_Sequence_Alignment_Tools
_Assessing_Performance_of_the_Underlying_Algorithms

clustal omega.pptx

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clustal omega.pptx