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Joseph Tiki R247549H

The document discusses scoring in Multiple Sequence Alignment (MSA), a key concept in bioinformatics used to align biological sequences. It outlines various scoring systems, including substitution matrices like BLOSUM62, match scores, mismatch penalties, and gap penalties, which help optimize alignments. Additionally, it highlights the importance of scoring in guiding MSA algorithms, such as ClustalW and T-Coffee, to achieve the best possible alignments.

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7 views8 pages

Joseph Tiki R247549H

The document discusses scoring in Multiple Sequence Alignment (MSA), a key concept in bioinformatics used to align biological sequences. It outlines various scoring systems, including substitution matrices like BLOSUM62, match scores, mismatch penalties, and gap penalties, which help optimize alignments. Additionally, it highlights the importance of scoring in guiding MSA algorithms, such as ClustalW and T-Coffee, to achieve the best possible alignments.

Uploaded by

luyandasydney25
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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JOSEPH TIKI R247549H 1

 OBJECTIVES
 Introduction on scoring multiple sequence alignment
 Types of scoring systems used in MSA
 Scoring functions used in MSA
 Importance of Scoring in MSA Algorithms
SCORING MULTIPLE SEQUENCE
ALIGNMENT
 Introduction
 the concept of scoring in Multiple Sequence Alignment (MSA), an essential concept in
bioinformatics.
 MSA is widely used to align three or more biological sequences, such as DNA, RNA, or
proteins.
 This alignment helps in identifying evolutionary relationships, functional similarities,
and structural patterns among sequences.
 Scoring in MSA refers to the process of assigning numerical values to various events
in the alignment.
 These events include matches, mismatches, and gaps, and the goal is to optimize the
alignment based on the chosen scoring system.
 Is used to evaluate the quality of the alignment,
evolutionary relationships and protein structure prediction.
 Types of scoring systems used in MSA:
 1. Substitution matrix e.g. BLOSUM62 matrix is commonly
used for protein sequence alignment.
 2. Gap penalties
 3. Match scores
 Scoring functions used in MSA:
 1. Sum-of-Pairs (SP) score, is a way of measure how good
the alignment is.
 2. COFFEE score
 1.Match Score- The score awarded when two residues (e.g.,
nucleotides in DNA or amino acids in proteins) from different
sequences are identical.
 WhyIt Matters: Match scores are essential for identifying
homologous regions across sequences.
 The more matches there are, the higher the alignment score,
indicating more conserved regions.
 2.Mismatch Penalty- The score assigned when two
residues are different in the alignment.
 Why It Matters:used to avoid aligning dissimilar residues,
encouraging the algorithm to find more biologically
meaningful alignments. High mismatch penalties will prevent
aligning very different residues unless absolutely necessary.
 3. Gap Penalty
A penalty assigned when gaps are introduced in the
alignment to optimize it.
 Gaps are necessary for accommodating insertions or
deletions that occurred during evolution.
 Types of Gap Penalties: Gap Opening Penalty, the penalty for
introducing a gap. Gap Extension Penalty, the penalty for
extending an existing gap.
 Substitution Matrices (for Protein Sequences)
 Substitution matrices, such as BLOSUM and PAM, are
designed based on evolutionary studies of amino acid
substitution frequencies.
 BLOSUM Matrix: BLOSUM (Blocks Substitution Matrix) is a matrix that
assigns positive or negative scores based on the likelihood of one amino
acid substituting for another during evolution.
 It is commonly used for protein alignments.
 Importance of Scoring in MSA Algorithms
 Scoring helps guide the MSA algorithm in identifying the optimal alignment.
 Popular MSA algorithms include ClustalW, T-Coffee, and MAFFT, which all use
scoring systems to assess and refine alignments.
 The key objective of these algorithms is to maximize the overall alignment
score.
 Dynamic Programming Algorithms: Scoring plays an essential role in
dynamic programming algorithms like Needleman-Wunsch and Smith-
Waterman, which break down the alignment problem into smaller
subproblems.
 These algorithms use the scoring rules to evaluate and find the best
possible alignment.
SUM OF PAIRS SCORE AND TEA-
COFFEE SCORE
 AABCDGE
 AABCGBE
 AABCG- E
 Scoring rules, match =+1, mismatch=-1 and gap penalty=-2
THANK YOU

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