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Sequencing Alignment & Its Methods Group II

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11 views12 pages

Sequencing Alignment & Its Methods Group II

Uploaded by

shakirbacha41
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PPTX, PDF, TXT or read online on Scribd
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Name : Muhammad Maghaz

Roll No : (07)

Presentation Topic

Sterile Sides Of the Human Body,


Mechanism Of Bacterial Pathogenicity

Department Of Zoology, University of Swab


Sequence Alignment

• A sequence alignment is a way of arranging sequences of DNA,RNA or protein to identify the


regions of similarity
• Sequence alignment is considered the most essential step in comparing biological sequences.
• These regions of similarity are helpful in understanding the functional, structural, and
evolutionary relationships between the sequences.
• Sequence comparison is a crucial aspect of bioinformatics analysis that involves comparing
newly determined biological sequences with previously known sequences stored in databases.
Sequence Identity

• Sequence identity is the amount of characters which match exactly between


two different sequences.
• A: AAGGCTT
• B: AAGGC
• C:AAGGCAT
• Here identity(A,B)=100% (5 identical nucleotides/ min(length(A),length(B).
Identity(B,C)=100%, but identity(A,C)=85% ((6 identical nucleotides / 7)).
• So 100% identity does not mean two sequences are the same.
Sequence Similarity

• Sequence similarity is the percentage of aligned residues that ca be more


readily substituted for each other.
• Have similar physicochemical properties
SEQUENCING alignment algorithm / Methods
Global Alignment
• Global alignment is a method of
comparing two sequences, which aligns
the entire length of the sequences by
maximizing the overall similarity. This
method is used when comparing
sequences that are of the same length.

Local Alignment
• 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.
This is useful for identifying short
conserved regions in protein or
nucleotide sequences.
Types of sequence alignment

1. Pairwise Sequence Alignment


• Pairwise sequence alignment is the type
of sequence alignment that involves
aligning two sequences to identify the
optimal pairing of the sequences
• It is based on a scoring system that
assigns positive scores to matching
characters and negative scores to
mismatching characters or gaps.
• The main objective of pairwise
sequence alignment is to obtain the
highest possible score, which indicates
the degree of similarity between the Tool Used By Pairwise Sequence Alignment
two sequences. https://www.ebi.ac.uk/jdispatcher/psa/emboss_needle
Method For Generating PA
• There are three main methods for generating pairwise alignments:
• Dot-matrix method
• Dot matrix method, also known as the dot plot method, is a graphical method of sequence alignment
that involves comparing two sequences by plotting them in a two-dimensional matrix.
• In a dot matrix, two sequences that must be compared are plotted along a matrix’s horizontal and
vertical axes.
• The method then scans each residue of one sequence to identify similarities with all residues in the
other sequence.
• If a residue in one sequence matches a residue in the other sequence, a dot is placed in the
corresponding position in the matrix. Otherwise, the matrix position is left blank.
• If the two sequences being compared are highly similar, the dot plot will display as a single line along
the matrix's main diagonal. However,
• when the sequences are less similar, the dot plot will show more scattered dots with fewer diagonal
lines, indicating that the sequences share less similarity.
• • Dot plots can also find repeat elements in a single sequence. Short parallel lines above and
• below the main diagonal indicate the presence of repeats.
Types of sequence alignment

2. Multiple Sequence Alignment


• Multiple Sequence Alignment involves aligning multiple (three or more) biological
sequences to achieve optimal sequence matching.
• Multiple sequence alignments are used to identify conserved sequence regions and to
construct phylogenetic trees, which help us understand the functional and evolutionary
relationships between different species or groups of organisms.
Importance / Significance

Comparing newly determined biological sequences with previously known


sequences stored in databases
Identifying regions of similarity between sequences
Understanding the functional, structural, and evolutionary relationships
between sequences
Identifying conserved sequence patterns and motifs
Characterizing the functions of the sequences
Producing phylogenetic trees and obtaining information about the
evolutionary relationship between the sequences aligned
Predicting proteins’ secondary and tertiary structures
Predicting gene locations and new members of gene families
Developing degenerate PCR primers by analyzing multiple related
sequences
Tools

Tool Used For Pairwise Sequence Alignment


https://www.ebi.ac.uk/jdispatcher/psa/emboss_needle
Tool Used For MSA
https://www.ebi.ac.uk/jdispatcher/msa/muscle
Thank You For Your Kind Attention

❓
Questions Are Welcomed

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