Mastering Gap Penalties

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What is the default ktup for amino acids and nucleotides in FASTA?

6 for amino acids and 2 for nucleotides
2 for amino acids and 6 for nucleotides (correct)
8 for both amino acids and nucleotides
4 for both amino acids and nucleotides

What does E-value represent in sequence alignment?

The total number of alignments in a database
The number of gaps in the alignment
The number of alignments with a score ≥ S that one can expect to find by chance in a database of size N (correct)
The length of the query sequence

What factors affect the E-value in sequence alignment?

Database size and query length (correct)
Alignment score and number of gaps
Alignment length and database complexity
Number of mismatches and query sequence length

What does a lower E-value indicate in sequence alignment?

Better alignment (B) Signup and view all the answers

Which type of alignment is used to align two sequences?

Pairwise alignment (D) Signup and view all the answers

What is the purpose of alignment?

To identify regions of similarity (D) Signup and view all the answers

What is the main advantage of multiple sequence alignment?

It can find conserved segments across sequences (C) Signup and view all the answers

What is the main application of multiple sequence alignment?

Construction of phylogenetic trees (B) Signup and view all the answers

What is the difference between pairwise alignment and multiple alignment?

Multiple alignment aligns more than two sequences, while pairwise alignment aligns only two sequences (C) Signup and view all the answers

What is dynamic programming?

A method for solving complex problems by breaking them into simpler subproblems (C) Signup and view all the answers

What is the dot matrix or dot plot method?

A method for comparing sequences using a two-dimensional matrix (A) Signup and view all the answers

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) (A) Signup and view all the answers

What is the gap penalty value?

A value subtracted from the total alignment score to obtain the final alignment score (A) Signup and view all the answers

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 (C) Signup and view all the answers

What is the formula for calculating the raw alignment score?

S = ∑i + ∑m - Gi (C) Signup and view all the answers

What is the purpose of heuristic methods in alignment programs?

To estimate the best solution without considering every possible solution (A) Signup and view all the answers

What is the default word size for nucleotide sequences in BLAST?

11 (A) Signup and view all the answers

What is the purpose of the k-tuples (ktup) in FASTA?

To search for matching sequence patterns (C) Signup and view all the answers