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BIOLOGICAL DATABASES

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Navya Thalathoti
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4 views

BIOLOGICAL DATABASES

Uploaded by

Navya Thalathoti
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
You are on page 1/ 13

TOPIC:

pair wise sequence


alignment
CONTENTS
2

o Introduction

o Types of Pairwise Alignment

o Scoring Systems

o Global Alignment: Needleman-Wunsch


Algorithm

o Local Alignment: Smith-Waterman


Algorithm

o Applications of Pairwise Sequence


Alignment
INTRODUCTION
Pairwise sequence alignment is a method used to compare
two biological sequences, such as DNA, RNA, or proteins, to
identify regions of similarity. The goal is to align the
sequences in a way that maximizes their similarity based
on matching nucleotides or amino acids, allowing
researchers to identify functional, structural, or evolutionary
relationships between them..
TYPES OF
4 PA I R W I S E
ALIGNMENT
Global Alignment: Local Alignment:
•Compares two sequences over their • Finds regions of similarity
entire length. within parts of the
sequences.
•Useful when the sequences are similar
• Used when comparing
in length and composition. sequences that differ
significantly in length.
•Example Algorithm: Needleman-
• Example Algorithm:
Wunsch.
Smith-Waterman.
5
Scoring Systems
Scoring systems are essential for
•Substitution Matrices: evaluating the quality of alignments.
• Matrices like PAM (Point Accepted
A typical scoring system includes
Mutation) and BLOSUM (Blocks match scores, mismatch penalties,
Substitution Matrix) provide scores and gap penalties.
for matching residues in protein
sequences. The choice of scoring parameters
•Gap Penalties: can significantly impact alignment
• Gap opening penalty: A score results.
that penalizes the introduction of a
gap.
• Gap extension penalty: A score
that penalizes extending an already
opened gap.
•Alignment Score:
• The total score is calculated based
on matches, mismatches, and
gaps, determining the optimal
Global Alignment:
Needleman- Wunsch
Algorithm:
 This algorithm aligns two sequences from
beginning to end (global alignment).
 Uses dynamic programming to fill a scoring
matrix and find the optimal alignment.

Steps:
 Initialization: Create a matrix with gaps
penalized.
 Matrix Filling: Fill the matrix using the
scoring system.
 Traceback: Follow the matrix from the
bottom-right corner to get the alignment.
Local Alignment: Smith-Waterman
•Algorithm
Smith-Waterman algorithm is used to
identify local regions of similarity
between sequences.
•Dynamic programming is also used,
but only the highest-scoring local
segment is reported.

•Steps:
1.Initialization: Initialize the matrix
with zeros.

2.Matrix Filling: Fill the matrix with


scores, allowing for negative scores.

3.Traceback: Start from the highest


8
Applications of Pairwise
Sequence
In Bioinformatics: Alignment
• To identify homologous sequences between species (e.g., gene sequences).

•In Evolutionary Biology:


• To infer evolutionary relationships and divergence times between species.

•In Functional Genomics:


• To predict the function of unknown genes or proteins by comparing them to known
sequences.

•In Comparative Genomics:


• To identify conserved regions across different species, providing insights into essential
genetic functions.
9
T O O L S F O R PA I R W I S E
SEQUENCE ALIGNMENT
•Common Software Tools:
 BLAST (Basic Local Alignment Search Tool): Finds
regions of local similarity.
 ClustalW: Often used for multiple sequence alignments
but can perform pairwise alignment as well.
 EMBOSS Needle & Water: Tools that implement
Needleman-Wunsch and Smith-Waterman algorithms
respectively.

•Online Resources:
 NCBI BLAST: A popular tool for aligning nucleotide or
protein sequences.
 EBI Tools: Provides access to a variety of alignment
tools.
Advantages and
10

Limitations
Advantages:
 Simple and efficient for comparing two
sequences.
 Provides insights into similarity and
differences between sequences quickly.

Limitations:
 Global alignment may not be ideal for
sequences with varying lengths.
 Pairwise alignment can miss relationships
present in multiple sequence comparisons.
 Computationally expensive for long
sequences.
Conclusion:
 Pairwise sequence alignment is essential in
comparative sequence analysis.
 Both global and local alignments serve different
purposes, depending on the sequences being
compared.

Future Perspectives:
 As genome databases expand, pairwise
alignment techniques will play a significant role
in personalized medicine, evolutionary studies,
and gene annotation.
12

References:
•Textbooks/Articles:
• "Bioinformatics: Sequence and
Genome Analysis" by David W.
Mount.
• Relevant journal articles on
sequence alignment algorithms.
•Web Resources:
• NCBI BLAST Tutorial.
• EBI Sequence Alignment Tools
Documentation.
T H A N K YO U

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