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Sequence Alignment Online Exam Quiz

Important questions about Sequence Alignment. Sequence Alignment MCQ questions with answers. Sequence Alignment exam questions and answers for students and interviews.

What is the length of a motif, in terms of amino acids residue?


A : a. 30- 60

B : b. 10- 20

C : c. 70- 90

D : d. 1- 10

On average, what is the length of a typical domain?


A : a. About 100 residues

B : b. About 300 residues

C : c. About 500 residues

D : d. About 900 residues

Which of the following is false about the ‘loop’ structure in proteins?


A : a. They connect helices and sheets

B : b. They are more tolerant of mutations

C : c. They are more flexible and can adopt multiple conformations

D : d. They are never the components of active sites

Which of the common structural motifs are described wrongly?


A : a. ?-hairpin – adjacent antiparallel strands

B : b. Greek key – 4 adjacent antiparallel strand

C : c. ?-?-? – 2 parallel strands connected by helix

D : d. ?-?-? – 2 antiparallel strands connected by helix

Which of the following least describes Long Loop ?-hairpins?


A : a. They are Often referred to as a ‘random coil’ conformation

B : b. Generally they are referred to as the ?-meander supersecondary structure

C : c. Loop looks similar to the Greek Letter ?

D : d. Wide-range of conformations with very specific sequence preferences

Motifs that can form ?/? horseshoes conformation are rich with which protein residue?


A : a. Proline

B : b. Arginine

C : c. Valine

D : d. Leucine

Which of the following wrongly describes protein domains?


A : a. They are made up of one secondary structure

B : b. Defined as independently foldable units

C : c. They are stable structures as compared to motifs

D : d. They are separated by linker regions

The protein structural motif domain- helix loop helix are contained by all of the following except ________


A : a. Scleraxis

B : b. Neurogenins

C : c. Transcription Factor 4

D : d. Leucine zipper

Which of the following is not the function of Short Linear Motifs?


A : a. Irreversible cleavage of the peptide at the SLiM

B : b. Reversible cleavage of the peptide at the SLiM

C : c. Moiety addition at targeted sites on SLiM

D : d. Structural modifications of the peptide backbone

In the zinc finger, which residues in this sequence motif form ligands to a zinc ion?


A : a. Cysteine and histidine

B : b. Cysteine and arginine

C : c. Histidine and proline

D : d. Histidine and arginine

While scanning for similarities in motifs, how regular expressions’ techniques work?


A : a. It represents a sequence family by a string of characters and further compares them

B : b. An algorithm similar to dynamic programming is used

C : c. Dot matrix analysis is used in this type of sequence analysis

D : d. Matrix analysis methods are used in this type

Which of the following best defines regular expressions?


A : a. They are made up of terms, operators and modifiers

B : b. They describe string or set of strings to find matching patterns

C : c. They are strictly restricted to alignment and corresponding score

D : d. They consist of set of rules for the connotations of various amino acid residues

In regular expressions, which of the following pair of pattern is wrongly matched with its significance?


A : a. [ ] – Or

B : b. { } – Not

C : c. ( ) – Repeats

D : d. Z – Any

In terminologies related to regular expressions which of the following is false about terms and operators?


A : a. Terms are strings or substrings

B : b. Operators combine terms and expressions

C : c. Operators do not have precedence

D : d. Operators have precedence like arithmetic operators

Emotif uses which databases for alignment of sequences?


A : a. BLOCKS and PRINTS databases




While analysing motif sequences, what is the major disadvantageous feature of PROSITE?


A : a. The database constructs profiles to complement some of the sequence patterns

B : b. The functional information of these patterns is primarily based on published literature

C : c. Some of the sequence patterns are too short to be specific

D : d. Lack of specificity about probability and variation and relation between them

Which of the following is not a characteristic of Fuzzy or approximate matches in regular expression?


A : a. This method is able to include more variant forms of a motif with a conserved function

B : b. the rule of matching is based on observations, not actual assumptions

C : c. with the more relaxed matching, there is increase of the noise level and false positives

D : d. the rule of matching is based on assumptions not actual observations

Which of the following is not a characteristic of exact matches in regular expression?


A : a. There must be a strict match of sequence patterns

B : b. Any variations in the query sequence from the predefined patterns are not allowed

C : c. Provide more permissive matching by allowing more flexible matching of residues of similar biochemical properties

D : d. Searching a motif database using this approach results in either a match or non-match

What does this representation mean- R.L.[EQD]?


A : a. An arginine- Amino acid- Leucine- Amino acid- Either Apartic acid, glutamic acid or glutamine

B : b. An arginine- Leucine- Either Apartic acid, glutamic acid or glutamine

C : c. An arginine- Leucine- Amino acid- Either Apartic acid, glutamic acid or glutamine

D : d. An arginine- Leucine- Apartic acid and glutamic acid and glutamine

Which of the following is not an advantage of Statistical models’ methods in analyzing protein motifs?


A : a. Sequence information is preserved from a multiple sequence alignment and expresses it with probabilistic models

B : b. Statistical models allow partial matches and compensate for unobserved sequence patterns using pseudo-counts

C : c. Statistical models have stronger predictive power than the regular expression based approach, even when they are derived from a limited set of sequences

D : d. The comparative flexibility is less in case of these methods when compared to regular expressions methods

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