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Questions and Answers
What is the primary purpose of PAM matrices in protein sequence analysis?
What is the primary purpose of PAM matrices in protein sequence analysis?
- To provide a framework for manual sequence alignment.
- To assess the likelihood of amino acid substitutions over evolutionary time. (correct)
- To identify phylogenetic trees without regard to sequence similarity.
- To predict the three-dimensional structure of proteins.
How are substitution matrices like PAM250 generated?
How are substitution matrices like PAM250 generated?
- By observing substitutions only in conserved regions.
- Using sequences of proteins with less than 50% identity.
- Through the manual alignment of sequences and analysis of amino acid substitution frequencies. (correct)
- By analyzing random substitutions between unrelated proteins.
What does the number in PAM matrices (such as PAM100) indicate?
What does the number in PAM matrices (such as PAM100) indicate?
- The total number of amino acids in a given protein structure.
- The number of substitutions observed in a family of proteins.
- The evolutionary distance between protein sequences. (correct)
- The range of sequence identities across all family members.
What scoring range indicates that a substitution is less likely than random?
What scoring range indicates that a substitution is less likely than random?
What major limitation do PAM matrices have regarding evolutionary rates?
What major limitation do PAM matrices have regarding evolutionary rates?
Which substitution matrix is typically preferred for local similarity searches?
Which substitution matrix is typically preferred for local similarity searches?
What is the correct approach when comparing closely related proteins?
What is the correct approach when comparing closely related proteins?
What technique is recommended for aligning sequences without gaps?
What technique is recommended for aligning sequences without gaps?
What is an excluded option regarding disulfide bridges in amino acids?
What is an excluded option regarding disulfide bridges in amino acids?
When is it appropriate to use matrices derived from observed substitutions?
When is it appropriate to use matrices derived from observed substitutions?
What limitation does the Slide Window method face when dealing with gaps?
What limitation does the Slide Window method face when dealing with gaps?
Which BLOSUM matrix is commonly used as the default for searching databases?
Which BLOSUM matrix is commonly used as the default for searching databases?
What is the primary characteristic of matrices derived from structure alignment?
What is the primary characteristic of matrices derived from structure alignment?
What score is assigned for a match when scoring insertions and deletions?
What score is assigned for a match when scoring insertions and deletions?
Which of the following is NOT a technique used for alignment?
Which of the following is NOT a technique used for alignment?
What is the disadvantage of manual alignment?
What is the disadvantage of manual alignment?
What is the purpose of the dot-matrix method?
What is the purpose of the dot-matrix method?
In a dot-matrix alignment, which step does a diagonal move through a dot represent?
In a dot-matrix alignment, which step does a diagonal move through a dot represent?
What value is assigned as the gap opening penalty in the scoring system?
What value is assigned as the gap opening penalty in the scoring system?
Why might protein alignment be guided by secondary and tertiary structures?
Why might protein alignment be guided by secondary and tertiary structures?
Which of the following best describes the function of the scoring system for insertions and deletions?
Which of the following best describes the function of the scoring system for insertions and deletions?
What does an E-value between 0.01 and 10 indicate about the match?
What does an E-value between 0.01 and 10 indicate about the match?
Which of the following statements about bit scores is true?
Which of the following statements about bit scores is true?
In the bit score calculation formula S’ = (λ × S − lnK)/ ln2, what does 'S' represent?
In the bit score calculation formula S’ = (λ × S − lnK)/ ln2, what does 'S' represent?
What is the consequence of an E-value greater than 10?
What is the consequence of an E-value greater than 10?
Which of the following is NOT a variant of the BLAST program?
Which of the following is NOT a variant of the BLAST program?
How does BLAST differ from FASTA in terms of sensitivity?
How does BLAST differ from FASTA in terms of sensitivity?
Which aspect of the BLAST program is related to speed?
Which aspect of the BLAST program is related to speed?
What role does the constant 'K' play in the bit score formula?
What role does the constant 'K' play in the bit score formula?
What type of phylogenetic tree reflects the amount of evolutionary change through proportional branch lengths?
What type of phylogenetic tree reflects the amount of evolutionary change through proportional branch lengths?
Which method is primarily concerned with maximizing the probability of observed data under a model of evolution?
Which method is primarily concerned with maximizing the probability of observed data under a model of evolution?
What is the primary purpose of a cladogram?
What is the primary purpose of a cladogram?
Which type of tree illustrates the timing of evolutionary events with all tips equidistant from the root?
Which type of tree illustrates the timing of evolutionary events with all tips equidistant from the root?
What characteristic distinguishes a split network from a simple phylogenetic tree?
What characteristic distinguishes a split network from a simple phylogenetic tree?
Which method estimates the posterior distribution of trees based on prior knowledge?
Which method estimates the posterior distribution of trees based on prior knowledge?
What type of phylogenetic tree is a general term for tree-like diagrams that illustrate clustering or hierarchical relationships?
What type of phylogenetic tree is a general term for tree-like diagrams that illustrate clustering or hierarchical relationships?
Which tree type does not have scaled branch lengths to evolutionary time?
Which tree type does not have scaled branch lengths to evolutionary time?
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Study Notes
Scoring Schemes or Weight Matrices
- PAM matrices (Percent Accepted Mutations) are derived from global alignments of protein families sharing at least 85% identity.
- PAM matrices are used to calculate the evolutionary distance between protein families.
- Construction of PAM matrices involves building a phylogenetic tree and ancestral sequences for each protein family.
- PAM matrices are based on observed substitutions, but the problem of "chicken and egg" arises.
- PAM matrices have limitations in considering different evolutionary rates between conserved and non-conserved regions.
- BLOSUM matrices (Blocks Substitution Matrix) are more commonly used for local similarity searches and have better performance than PAM matrices.
- BLOSUM matrices are based on aligned blocks of sequences that are more conserved than those used for PAM matrices.
- Higher BLOSUM or lower PAM matrices are better for comparing closely related proteins.
- Lower BLOSUM or higher PAM matrices are better for comparing distantly related proteins.
- BLOSUM62 is the commonly used matrix for database searching.
Sequence Alignment Techniques
- Manual alignment is a powerful tool for comparing similar sequences, but it is subjective and unscalable.
- Dot-matrix methods are used to identify regions of similarity between two sequences.
- Dot-matrix methods can be used to unravel information on the evolution of sequences.
- Dynamic programming algorithms, such as the Smith-Waterman algorithm, are used to find the optimal alignment between two sequences.
Gaps in Pair-wise Alignment
- Gaps are introduced in sequences to account for insertions and deletions.
- Insertion and deletion are common in evolution, and ignoring them can lead to incorrect alignment.
- Gap penalties are used to discourage the introduction of gaps in alignments.
- Gap opening penalties are higher than gap extension penalties.
BLAST
- BLAST (Basic Local Alignment Search Tool) is a powerful tool for searching databases for sequences that are similar to a query sequence.
- BLAST uses a substitution matrix and a hashing procedure to find matching words or sequences.
- BLAST is faster than FASTA and uses a low-complexity masking procedure to reduce false positives.
- BLAST is sensitive enough to find weak homologies, but lower sensitivity may improve speed.
Phylogenetic Tree Types
- Phylogenetic trees are used to represent the evolutionary relationship among species or organisms.
- A cladogram shows the order of branching without considering the evolutionary time.
- A phylogram shows the amount of evolutionary divergence based on branch lengths.
- An ultrametric tree or chronogram shows the timing of evolution where all tips are equidistant from the root.
- A dendrogram is a general term for tree-like diagrams used to illustrate clustering or hierarchical relationships.
Character-Based Methods
- Maximum parsimony (MP) methods select the tree that requires the least number of evolutionary changes.
- Maximum likelihood (ML) methods find the tree that maximizes the probability of the observed data given a model of evolution.
- Bayesian inference is a probabilistic approach that uses the likelihood of observed data and prior knowledge to estimate the posterior distribution of trees.
Clustering-Based Methods
- Hierarchical clustering groups sequences into clusters and produces dendrograms that resemble phylogenetic trees, but may not reflect true evolutionary relationships.
Network-Based Methods
- Split networks can handle complex relationships, such as hybridization or gene flow, that are not easily represented by a simple tree.
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