79. Which one of the following is true for PAM250 Scoring Matrix?
A. It is used for structural database search.
B. It is based on an evolutionary model that predicts the types of amino acid changes over long
periods of time.
C. It can be used to score alignments for nucleotide changes over long periods of time.
D. It can distinguish synonymous and non-synomynous mutations.

Introduction:

In bioinformatics, scoring matrices like PAM250 are essential tools for aligning protein sequences. The PAM250 matrix is part of the Point Accepted Mutation (PAM) series, which is based on an evolutionary model that predicts how amino acid substitutions accumulate over time. Understanding how these matrices work helps in tasks like comparing protein sequences, identifying conserved regions, and studying evolutionary relationships.

In this article, we will focus on the PAM250 scoring matrix, specifically explaining its role in sequence alignment and why it is used for modeling amino acid changes over long periods of evolutionary time.

What is PAM250 Scoring Matrix?

1. PAM Series:

   • The PAM (Point Accepted Mutation) matrix family was developed by Margaret Dayhoff and is based on the assumption that the frequency of amino acid substitutions can be described by evolutionary changes over a specific period. The number 250 in PAM250 refers to the number of amino acid substitutions expected in 250 evolutionary steps (or generations).

2. PAM250 Matrix:

   • The PAM250 matrix is a scoring system used in sequence alignment algorithms to compare protein sequences. It reflects the likelihood of one amino acid being substituted for another during evolution. The higher the score, the more likely the substitution is considered evolutionarily acceptable.

3. Evolutionary Model:

   • The PAM250 matrix is based on an evolutionary model that predicts the types of amino acid changes that would be likely over long periods of evolutionary history. It provides a numerical value for each possible amino acid pair, which can be used to score the similarity between two aligned sequences.

Key Feature of PAM250 Matrix:

• B. It is based on an evolutionary model that predicts the types of amino acid changes over long periods of time.

Correct Answer:

B. It is based on an evolutionary model that predicts the types of amino acid changes over long periods of time.

Why Other Options Are Incorrect:

• A. It is used for structural database search: While PAM matrices are commonly used for sequence alignment, they are not primarily designed for structural database searches. Structural searches typically use different scoring methods that account for 3D protein structures.

• C. It can be used to score alignments for nucleotide changes over long periods of time: The PAM250 matrix is specifically designed for protein sequences and not for nucleotide alignments. Nucleotide sequences typically use scoring systems like BLOSUM or custom nucleotide substitution matrices.

• D. It can distinguish synonymous and non-synonymous mutations: The PAM250 matrix does not specifically distinguish between synonymous (no amino acid change) and non-synonymous (amino acid change) mutations. This distinction is often made using different tools designed for nucleotide-level analysis.

Conclusion:

The PAM250 scoring matrix plays a crucial role in protein sequence alignment by providing a way to quantify amino acid substitutions based on evolutionary principles. The matrix is grounded in an evolutionary model that predicts the likelihood of amino acid changes over time, making it invaluable in comparative genomics and evolutionary biology studies. By understanding how these matrices work, bioinformaticians can more accurately align and compare protein sequences, shedding light on evolutionary relationships and functional conservation.