152. Given below are two statements:
Statement I: An alignment is generated by starting at the ends of the two sequences and
attempting to match all possible pairs of characters between the sequences and by following a
scoring scheme for matches, mismatches, and gaps.
Statement II: For proteins, an amino acid substitution matrix, such as the Dayhoff percent accepted
mutation matrix 250 (PAM250) or Blosum substitution matrix 62 (BLOSUM62) is used to score
matches and mismatches.choose the most appropriate answer from the options
given below:
A. Both Statement I and Statement II are correct.
B. Both Statement I and Statement II are incorrect.
C. Statement I is correct but Statement II is incorrect.
D. Statement I is incorrect but Statement II is correct.

 

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Sequence Alignment and Scoring Matrices: Clarifying Key Concepts

In bioinformatics, sequence alignment is a foundational technique used to identify similarities between biological sequences (DNA, RNA, or protein). It helps in functional analysis, structural prediction, and evolutionary studies. However, accuracy in how alignments are generated and scored is crucial.

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Statement Analysis

Statement I:

“An alignment is generated by starting at the ends of the two sequences and attempting to match all possible pairs of characters between the sequences and by following a scoring scheme for matches, mismatches, and gaps.”

• Assessment: Incorrect

• Explanation: Alignments are not generated by merely starting at the ends and matching all possible pairs. In computational biology, algorithms like Needleman-Wunsch (global alignment) and Smith-Waterman (local alignment) use dynamic programming techniques, not brute force pairwise matching. These methods optimize a scoring matrix for gaps, matches, and mismatches.

Statement II:

“For proteins, an amino acid substitution matrix, such as the Dayhoff percent accepted mutation matrix 250 (PAM250) or Blosum substitution matrix 62 (BLOSUM62) is used to score matches and mismatches.”

• Assessment: Correct

• Explanation: This is accurate. Protein alignments use substitution matrices to score amino acid replacements based on evolutionary probability. PAM and BLOSUM matrices are well-established tools. For instance:

  • PAM250 models substitutions in sequences with higher divergence.

  • BLOSUM62 is widely used for sequences with ~62% similarity.

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Conclusion

• Statement I is incorrect due to its inaccurate description of alignment methodology.

• Statement II is correct and reflects standard bioinformatics practices.

Correct Answer: D. Statement I is incorrect but Statement II is correct.