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Questions and Answers
What is the primary difference between PAM and BLOSUM matrices?
The Needleman-Wunsch algorithm is a type of dynamic programming method used for local sequence alignment.
False
What does dynamic programming mean in the context of sequence alignment?
It refers to a systematic method for solving alignment problems by breaking them into simpler subproblems and utilizing previously computed solutions.
PAM and BLOSUM matrices are both used in __________ calculations for sequence alignment.
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Match the following algorithms or matrices with their characteristic:
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What do substitution matrices primarily describe?
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Negative values in a substitution matrix indicate that an occurrence of amino acid substitution is likely to be evolutionary.
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What are the two commonly used substitution matrices mentioned?
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The basic rules for scoring matrices were first put forward by _____ in 1978.
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Match the following terms with their corresponding definitions:
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How can increasing the window size affect aligned strings?
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A substitution matrix uses a simple scoring method of only positive numbers.
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What does the scoring system in alignment utilize to devise scores?
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What is the main advantage of heuristic methods over dynamic programming?
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A dot plot requires sequences to be aligned before it can show matches.
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What do the dots in a dot plot represent?
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The method of alignment that specifies biological evolution through models is known as __________.
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Match the following scoring systems to their respective descriptions:
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Which alignment method allows for gaps to be introduced?
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The background noise in biological sequences is low.
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How do you determine the maximal alignment in a dot plot?
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Study Notes
Learning Outcomes
- Compute alignment scores considering gap penalties.
- Understand three methods for aligning two sequences: graphical, dynamic programming, and dot matrix.
- Distinguish between PAM and BLOSUM substitution matrices.
- Describe the dynamic programming concept and its application in sequence alignment.
- Differentiate between Needleman-Wunsch and Smith-Waterman algorithms.
Alignment Methods
- Graphical method allows visual assessment of alignment quality and type.
- Dynamic programming provides a mathematically rigorous solution for optimal sequence alignment.
- Increasing window size in dot plot reduces noise, enhancing visibility of aligned regions.
Scoring Alignments
- Use a score matrix (1 for match, 0 for mismatch) instead of dots for scoring alignments.
- Score is calculated by summing values along the optimal path in the matrix.
Substitution Matrices
- Substitution matrices quantify the likelihood of one character changing to another over time.
- Amino acid substitutions occur at different probabilities; exchanges like Asp to Glu are common, while Asp to Trp is rare.
- Matrices reflect evolutionary events, indicating both coincidental (negative scores) and evolutionary (positive scores) occurrences.
- Dayhoff's basic scoring rules in 1978 laid the groundwork for scoring matrices like PAM and BLOSUM.
Dynamic Programming
- Dynamic programming (DP) algorithms solve complex problems through a heuristic recursive process.
- They construct solutions from previously found sub-solutions using divide and conquer tactics.
- Faster than complete dynamic programming while still providing approximations.
Dot Plot Method
- The dot plot visually displays similarities between two sequence strings using a matrix.
- Matches are indicated with dots, while mismatches are left blank, providing initial confirmation of alignment.
- Long diagonal runs in the dot plot indicate potential maximal alignments.
Example of Sequence Alignment
- Given sequences demonstrate multiple potential alignments, each with 8 matches and 4 gaps, showcasing the flexibility of gap introduction.
- Gaps can represent insertions or deletions, illustrated by jumps in the dot plot.
Noise in Biological Sequences
- Biological sequences exhibit high background noise, affecting alignment accuracy.
- The dot plot method helps in revealing true alignments against random background variability.
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Description
Test your knowledge on pairwise sequence alignments in bioinformatics. This quiz will cover scoring for alignments and the methods used to align two sequences. Perfect for students of BIOC 3265 at UWI Cave Hill.
