Bioinformatics Sequence Alignments Exam Questions with Answers Latest Update (Graded A+)
Sequence alignments - Answers identification of residue-residue correspondence (pattern recognition)
Dotplot - Answers simple picture that gives an overview of the similarities between two sequences, but does...
Measures of nucleotide sequence similarity include ________ ________ for matches and mismatches -
Answers point systems
Protein sequence scoring schemes - Answers PAM, BLOSUM
PAM (Point Accepted Mutation) - Answers measure of sequence divergence
1 PAM = 1% accepted mutation (99% identity)
PAM250 (20% overall identity) is the lowest sequence similarity
BLOSUM (BLOcks SUbstitution Matrix) - Answers based on substitution patterns in conserved motifs
from the BLOCKS database
62% threshold is frequently used (BLOSUM62)
Which scoring schemes to use with short alignments that are highly similar - Answers PAM40
BLOSUM90
Which scoring schemes to use when detecting members of a protein family - Answers PAM160
BLOSUM80
Which scoring schemes to use with longer alignments of more divergent sequences - Answers PAM250
BLOSUM30
Most effective scoring scheme in finding all potential similarities; NCBI BLAST default - Answers
BLOSUM62
Gap opening penalty (G) - Answers the cost of creating a gap
Gap extension penalty (L) - Answers the cost of extending a gap by one position
Affine gap penalty - Answers (G + Ln); n = length of gap
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