Sequence Alignment MCQs

Welcome to our comprehensive collection of Multiple Choice Questions (MCQs) on Sequence Alignment, a fundamental topic in the field of Bioinformatics. Whether you're preparing for competitive exams, honing your problem-solving skills, or simply looking to enhance your abilities in this field, our Sequence Alignment MCQs are designed to help you grasp the core concepts and excel in solving problems.

In this section, you'll find a wide range of Sequence Alignment mcq questions that explore various aspects of Sequence Alignment problems. Each MCQ is crafted to challenge your understanding of Sequence Alignment principles, enabling you to refine your problem-solving techniques. Whether you're a student aiming to ace Bioinformatics tests, a job seeker preparing for interviews, or someone simply interested in sharpening their skills, our Sequence Alignment MCQs are your pathway to success in mastering this essential Bioinformatics topic.

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Sequence Alignment MCQs | Page 3 of 15

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Q21.
Which of the following is not an advantage of Statistical models’ methods in analyzing protein motifs?

a.

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

b.

Statistical models allow partial matches and compensate for unobserved sequence patterns using pseudo-counts

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.

The comparative flexibility is less in case of these methods when compared to regular expressions methods

Discuss
Answer: (d).The comparative flexibility is less in case of these methods when compared to regular expressions methods
Q22.
For motif scanning which of the following programs or databases is for regulated sites curated from scientific literature?

a.

ENSEMBL

b.

ORegAnno

c.

MAST

d.

Clover

Discuss
Answer: (b).ORegAnno
Q23.
Which of the following is not an advantageous feature or algorithm of the database PRINTS?

a.

This program breaks down a motif into even smaller non-overlapping units called ‘fingerprints’, which are represented by unweighted PSSMs

b.

To define a motif, at least a majority of fingerprints are required to match with a query sequence

c.

A query that has simultaneous high-scoring matches to a majority of fingerprints belonging to a motif is a good indication of containing the functional motif

d.

The difficulty to recognize short motifs when they reach the size of single fingerprints

Discuss
Answer: (d).The difficulty to recognize short motifs when they reach the size of single fingerprints
Q24.
In which of the following multipurpose packages Gibbs sampling algorithm is used?

a.

Consensus

b.

BEST

c.

AlignACE

d.

PhyloCon

Discuss
Answer: (c).AlignACE
Q25.
Which of the following is untrue in case of the database BLOCKS?

a.

The alignments are automatically generated using the same data sets used for deriving the BLOSUM matrices

b.

The derived ungapped alignments are called ‘blocks’, which are usually longer than motifs, are subsequently converted to PSSMs

c.

A weighting scheme and pseudo counts are subsequently applied to the PSSMs to account for underrepresented and unobserved residues in alignments

d.

The functional annotation of blocks is not consistent with that for the motifs

Discuss
Answer: (d).The functional annotation of blocks is not consistent with that for the motifs
Q26.
Which of the following is false in case of the database Pfam and its algorithm?

a.

Each motif or domain is represented by an HMM profile generated from the seed alignment of a number of conserved homologous proteins

b.

Since the probability scoring mechanism is more complex in HMM than in a profile-based approach the use of HMM yields further increases in sensitivity of the database matches

c.

Pfam-B only contains sequence families not covered in Pfam

d.

The functional annotation of motifs in Pfam-A is often related to that in UNIPROT

Discuss
Answer: (d).The functional annotation of motifs in Pfam-A is often related to that in UNIPROT
Q27.
Which of the following is false in case of the database SMART and its algorithm?

a.

Contains HMM profiles constructed from manually refined protein domain alignments

b.

Alignments in the database are built based on tertiary structures whenever available or based on PSI-BLAST profiles

c.

Alignments are further checked but not refined by human annotators before HMM profile construction

d.

SMART stands for Simple Modular Architecture Research Tool

Discuss
Answer: (c).Alignments are further checked but not refined by human annotators before HMM profile construction
Q28.
Which of the following is false in case of the database InterPro and its algorithm?

a.

InterPro is an integrated pattern database designed to unify multiple databases for protein domains and functional sites

b.

This database integrates information from PROSITE, Pfam, PRINTS, ProDom, and SMART databases

c.

Only overlapping motifs and domains in a protein sequence derived by all five databases are included

d.

All the motifs and domains in a protein sequence derived by all five databases are included

Discuss
Answer: (d).All the motifs and domains in a protein sequence derived by all five databases are included
Q29.
Which of the following is false in case of the CDART and its algorithm?

a.

CDART is a domain search program that combines the results from RPS-BLAST, SMART, and Pfam

b.

The program is now an integral part of the regular BLAST search function

c.

CDART is a substitute for individual database searches

d.

It stands for Conserved Domain Architecture

Discuss
Answer: (c).CDART is a substitute for individual database searches
Q30.
Point out the wrong or irrelevant mathematical method in motif analysis.

a.

Enumeration

b.

Probabilistic Optimization

c.

Deterministic Optimization

d.

Literature mining

Discuss
Answer: (d).Literature mining
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