Bioinformatics Sequence Alignments Exam Questions with Answers Latest Update (Graded A+)

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 not provide statistical measurement Dotplot: multiple parallel lines signify - Answers repetitive sequence Dotplot: cross signifies - Answers palindrome 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 Global alignment algorithms - Answers compare two sequences along their entire length, and are most applicable to highly similar sequences Local alignment algorithms - Answers find the most similar regions in two sequences, and are best for sequences that share some degree of similarity or for sequences of different lengths Global alignment algorithms are based on the mathematical technique called ____________ - Answers dynamic programming (guaranteed to give an optimal global alignment) Smith-Waterman algorithm - Answers most rigorous local alignment algorithm by which regions of two protein or DNA sequences can be aligned Smith-Waterman algorithm pros and cons - Answers Pro: Guaranteed to find the optimal alignment(s) between two sequences Con: Relatively slow BLAST (Basic Local Alignment Search Tool) - Answers rapid, heuristic version of the Smith-Waterman algorithm; takes word size "w" and determines all instances of the words in a query sequence that occur in any sequence in the database HSP (High-Scoring Segment Pair) - Answers consists of two sequence segments whose alignment is locally maximal and meets the score threshold S P value - Answers probability that the observed match could have happened by chance; used by BLAST E value - Answers expected number of matches that give the same Z score or better if the database is searched with a random sequence; used by most databases Main NCBI tool for comparing a protein or DNA sequence to other sequences in databases - Answers BLAST Five main BLAST programs - Answers BLASTP, BLASTN, BLASTX, TBLASTN, TBLASTX BLASTP - Answers protein vs protein database BLASTN - Answers nucleotide vs nucleotide database BLASTX - Answers translated nucleotide vs protein database TBLASTN - Answers translate every DNA sequence in a database into six potential proteins, and then compare protein query against each translated protein