Gene Prediction and Annotation: Master the Fundamentals

Question 1

Which commonly used gene prediction algorithm employs a statistical model to identify coding regions?

Accepted Answer

Hidden Markov Model (HMM)

Answer

Support Vector Machine (SVM)

Answer

k-nearest neighbors (k-NN)

Answer

Decision Tree

Question 2

What is the primary purpose of functional annotation in gene prediction?

Accepted Answer

Ascribing functions to genes and their products

Answer

Determining chromosomal locations of genes

Answer

Predicting protein structures

Answer

Mapping genetic variations

Question 3

Which approach is NOT employed for computational gene prediction?

Accepted Answer

Wet-lab experimentation

Answer

Ab initio prediction

Answer

Comparative genomics

Answer

Machine learning

Question 4

Which of the following is NOT a commonly used gene prediction method?

Accepted Answer

ORF-based prediction

Answer

Ab initio prediction

Answer

Homology-based prediction

Answer

Motif-based prediction

Question 5

What is the primary goal of gene annotation?

Accepted Answer

Determine the function of a gene

Answer

Identify the sequence features of a gene

Answer

Predict the expression pattern of a gene

Answer

Annotate the genome with regulatory elements

Question 6

What is the term for a sequence motif that is often associated with regulatory elements?

Accepted Answer

Consensus sequence

Answer

Promoter sequence

Answer

Enhancer sequence

Answer

Terminator sequence

Question 7

Which of the following software tools is used for de novo gene prediction?

Accepted Answer

GeneMarkS

Answer

BLAST

Answer

InterProScan

Answer

Ensembl

Question 8

What is the name of the process by which a gene's sequence is translated into a protein?

Accepted Answer

Translation

Answer

Transcription

Answer

Replication

Answer

Recombination

Question 9

What is the primary purpose of functional annotation in bioinformatics?

Accepted Answer

To identify potential functions of genes and proteins

Answer

To determine the location of genes on a chromosome

Answer

To predict the structure of proteins

Answer

To identify regulatory elements

Question 10

What is the term for the region of DNA that regulates gene expression?

Accepted Answer

Promoter

Answer

Exon

Answer

Intron

Answer

Terminator

Question 11

What is the main advantage of using comparative genomics for gene prediction?

Accepted Answer

Conserved sequences are more likely to be functional

Answer

It can predict genes in regions with low sequence conservation

Answer

It can identify genes that are not conserved across species

Answer

It is faster than other gene prediction methods

Question 12

Which of the following algorithms is commonly used for ab initio gene prediction?

Accepted Answer

Hidden Markov Models (HMMs)

Answer

Support Vector Machines (SVMs)

Answer

k-Nearest Neighbors (k-NN)

Answer

Random Forests

Question 13

What is the primary responsibility of Gene Ontology (GO) in gene annotation?

Accepted Answer

To provide a standardized vocabulary for describing gene functions

Answer

To identify orthologous genes across species

Answer

To predict the structure of proteins

Answer

To generate multiple sequence alignments

Question 14

Which software tool is widely used for gene annotation?

Accepted Answer

BLAST

Answer

ClustalW

Answer

RAxML

Answer

ImageJ

Question 15

What is the name of the technique used to identify regulatory elements by analyzing DNA sequences?

Accepted Answer

Motif discovery

Answer

Primer design

Answer

PCR amplification

Answer

DNA sequencing

Question 16

Which of the following is NOT a widely used gene prediction tool?

Accepted Answer

BLAST

Answer

Genscan

Answer

HMMER

Answer

GeneMark

Question 17

What is the primary aim of gene annotation?

Accepted Answer

To identify the function and regulation of genes

Answer

To predict gene expression levels

Answer

To identify genetic variants associated with disease

Answer

To develop new drugs

Question 18

What is the role of comparative genomics in gene prediction?

Accepted Answer

To identify conserved regions that likely contain genes

Answer

To determine the evolutionary history of genes

Answer

To predict gene expression patterns

Answer

To develop new gene therapies

Question 19

What is the distinction between supervised and unsupervised machine learning in the context of gene prediction?

Accepted Answer

Supervised learning requires labeled data, while unsupervised learning does not.

Answer

Supervised learning is more accurate than unsupervised learning.

Answer

Unsupervised learning can be used to discover hidden patterns in data.

Answer

Supervised learning is used for classification tasks, while unsupervised learning is used for regression tasks.

Question 20

In gene prediction for non-model organisms, what are the key advantages and limitations of comparative genomics?

Accepted Answer

Advantage: Allows for identification of conserved genes through cross-species comparisons.

Accepted Answer

Limitation: May not accurately predict gene function, as sequence similarity does not always indicate functional equivalence.

Answer

Limitation: Not applicable to non-model organisms due to lack of genomic data for comparison.

Answer

Advantage: Requires minimal genomic data, making it suitable for organisms with limited information.

Question 21

Which method of gene prediction relies on sequence similarity between genes in related species?

Accepted Answer

Comparative genomics

Answer

Proteomics

Answer

De novo gene prediction

Answer

Gene expression profiling

Question 22

What is a key step in gene annotation?

Accepted Answer

Assigning putative functions to predicted genes based on their sequence characteristics and similarity to known genes.

Answer

Identifying regulatory elements.

Answer

Predicting protein structures.

Answer

Evaluating gene expression levels.

Question 23

Why is it important to identify regulatory elements in gene prediction?

Accepted Answer

Understanding the mechanisms that control gene expression.

Answer

Predicting protein-protein interactions.

Answer

Determining gene dosage.

Question 24

What is the fundamental difference between gene prediction and gene annotation?

Accepted Answer

Gene prediction identifies potential gene locations, while gene annotation assigns functions to those predicted genes.

Answer

Gene prediction utilizes computational methods, while gene annotation is an experimental process.

Answer

Gene prediction is typically more accurate than gene annotation.

Question 25

Which of the following tools is commonly used for automated gene annotation?

Accepted Answer

BLAST

Answer

ClustalW

Answer

R

Answer

PHYML

Question 26

Why should alternative splicing be considered during gene prediction?

Accepted Answer

It can lead to the production of multiple protein isoforms from a single gene.

Answer

It is only relevant for eukaryotic genes.

Answer

It can reduce the accuracy of gene expression profiling.

Question 27

Which factors can impact the accuracy of gene prediction?

Accepted Answer

Gene expression level, availability of reference genomes, and sequence complexity

Answer

Only sequence complexity

Answer

None of the above

Answer

Only gene expression level