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This quiz contains multiple-choice problems on sequence homology versus sequence similarity, methods and statistical significance of sequence alignment.
Which of the following is incorrect regarding pair wise sequence alignment?
The most fundamental process in this type of comparison is sequence alignment
It is an important first step toward structural and functional analysis of newly determined sequences
This is the process by which sequences are compared by searching for common character patterns and establishing residue-residue correspondence among related sequences
It is the process of aligning multiple sequences
Which of the following is incorrect about evolution?
The macromolecules can be considered molecular fossils that encode the history of millions of years of evolution
The building blocks of these biological macromolecules, nucleotide bases, and amino acids form linear sequences that determine the primary structure of the molecules
DNA and proteins are products of evolution
The molecular sequences barely undergo changes
The presence of evolutionary traces is because some of the residues that perform vital functional and structural roles tend to be preserved by natural selection; other residues that may be less crucial for structure and function tend to mutate more frequently. True or false?
True
False
The degree of sequence variation in the alignment reveals the evolutionary relatedness of different sequences. In contrast, the conservation between sequences reflects the evolutionary changes as substitutions, insertions, and deletions. True or false?
True
False
It is highly __ that the extensive similarities between two sequences have been acquired randomly, meaning that the sequences must have derived from a common evolutionary origin.
Unlikely
Possible
Likely
Relevant
It is possible in some cases that two sequences have derived from a common ancestor but may have diverged to such an extent that the common ancestral relationships are not recognizable at the sequence level. True or false?
True
False
Which of the following is incorrect regarding sequence homology?
Two sequences can homologous relationship even if have do not have common origin
It is an important concept in sequence analysis
When two sequences are descended from a common evolutionary origin, they are said to have a homologous relationship
When two sequences are descended from a common evolutionary origin, they are said to share homology
Sequence similarity can be quantified using __ homology in a __ statement.
percentages, quantitative
percentages, qualitative
ratios, qualitative
ratios, quantitative
Shorter sequences require higher cutoffs for inferring homologous relationships than longer sequences. True or false?
True
False
Sequence similarity and sequence identity are synonymous for nucleotide sequences and protein sequences. True or false?
True
False
Alignment algorithms, both global and local, are fundamentally similar and only differ in the optimization strategy used in aligning similar residues. True or false?
True
False
In a dot matrix, two sequences to be compared are written in the __ of the matrix.
Horizontal and vertical axes
Two parallel horizontal axes
Two parallel vertical axes
Horizontal axis (one preceding another)
When two sequences have substantial regions of similarity, many dots line up to form contiguous __ lines.
Crossings on
Horizontal
Diagonal
Vertical
If the selected window size is too long, the sensitivity of the alignment is lost. True or false?
True
False
When comparing __ sequences using the dot matrix method, viz., the __, a problem exists.
small, amplification
large, amplification
small, high noise level
large, high noise level
