18 Questions
What is the default ktup for amino acids and nucleotides in FASTA?
2 for amino acids and 6 for nucleotides
What does E-value represent in sequence alignment?
The number of alignments with a score ≥ S that one can expect to find by chance in a database of size N
What factors affect the E-value in sequence alignment?
Database size and query length
What does a lower E-value indicate in sequence alignment?
Better alignment
Which type of alignment is used to align two sequences?
Pairwise alignment
What is the purpose of alignment?
To identify regions of similarity
What is the main advantage of multiple sequence alignment?
It can find conserved segments across sequences
What is the main application of multiple sequence alignment?
Construction of phylogenetic trees
What is the difference between pairwise alignment and multiple alignment?
Multiple alignment aligns more than two sequences, while pairwise alignment aligns only two sequences
What is dynamic programming?
A method for solving complex problems by breaking them into simpler subproblems
What is the dot matrix or dot plot method?
A method for comparing sequences using a two-dimensional matrix
What is the purpose of introducing gaps in sequence alignment?
To improve alignment when one of the sequences has gained or lost sequences (insertion/deletion)
What is the gap penalty value?
A value subtracted from the total alignment score to obtain the final alignment score
What is the default gap-opening penalty and gap-extension penalty used in many alignment programs?
-10 for gap-opening penalty and -1 for gap-extension penalty
What is the formula for calculating the raw alignment score?
S = ∑i + ∑m - Gi
What is the purpose of heuristic methods in alignment programs?
To estimate the best solution without considering every possible solution
What is the default word size for nucleotide sequences in BLAST?
11
What is the purpose of the k-tuples (ktup) in FASTA?
To search for matching sequence patterns
Test your knowledge on gap penalties in sequence alignment with this quiz! Learn about the differences between gap-opening and gap-extension penalties, default values used, and how to calculate the total gap penalty. By the end of this quiz, you'll be a pro at understanding gap penalties in sequence alignment.
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