Flashcards on Bioinformatics: Sequence Analysis and Prediction
Bioinformatics: Sequence Analysis and Prediction Guide for Students
Tap to flip · Swipe to navigate
Protein sequence scoring matrices
23 cards
Card 1
Question: What biological factors influence protein scoring matrices?
Answer: Conservation (absolute and conservative substitutions), residue frequency (rare vs common residues), and evolution (different matrices for different e
Card 2
Question: What does 'conservation' account for in scoring matrices?
Answer: It accounts for absolute conservation and conservative substitutions, representing which residues may be substituted by which other residues.
Card 3
Question: How does residue frequency affect scoring matrices?
Answer: Scoring takes into account how often particular residues occur; rare residues are weighted differently from common residues.
Card 4
Question: Why are different scoring matrices used for different evolutionary rates?
Answer: Because substitution patterns vary with evolutionary distance, different matrices better reflect replacement probabilities at different rates of evolu
Card 5
Question: What principle explains higher replaceability among certain amino acids?
Answer: Amino acids are more likely to replace others within the same physico-chemical groups, so replaceability is higher within those groups.
Card 6
Question: What is BLOSUM62?
Answer: A specific amino-acid scoring matrix (BLOSUM62) that gives substitution scores for each pair of amino acids.
Card 7
Question: How are scores in matrices like BLOSUM62 calculated conceptually?
Answer: They represent log-odds ratios comparing observed replacement frequencies to expected frequencies under random replacement.
Card 8
Question: What does a positive score in a substitution matrix indicate?
Answer: That two residues replace each other more often than expected by chance.
Card 9
Question: What does a negative score in a substitution matrix indicate?
Answer: That two residues replace each other less often than expected by chance.
Card 10
Question: What is the log-odds score S_{i,j} for two residues i and j in a scoring matrix formula?
Answer: S_{i,j} = log (q_{i,j} / (p_i p_j)), where q_{i,j} is the observed alignment frequency of i with j and p_i, p_j are background frequencies of residues