Part B

Ph.D Question paper

Course Title: Bioinformatics
Course Code: C

QUESTION 1 Which of the following is true regarding the methods of gene prediction?
Option A They solely consist of a type called ab initio–based methods
Option B The ab initio–based approach predicts genes based on the given sequence alone
Option C The ab initio–based approach predicts genes based on the given sequence and
relative homology data
Option D They solely consist of a type called homology-based approaches

QUESTION 2 Which of the following is a wrong about AutoMotif?

Option A It doesn’t use SVM approach
Option B It is a web server predicting protein sequence motifs
Option C In this process, the query sequence is chopped up into a number of overlapping
fragments
Option D The overlapping fragments from are query sequence are fed into different
kernels (similar to nodes)

QUESTION 3 An understanding of the importance of different factors in a particular interaction

is important if confidence in the results is required. Which of the following are
not those factors?
Option A Shape
Option B Hydrophobicity
Option C pH
Option D Electrostatics

QUESTION 4 Which of the following is a wrong about AutoMotif?

Option A It is a web server predicting protein sequence motifs
Option B It doesn’t use SVM approach
Option C In this process, the query sequence is chopped up into a number of overlapping
fragments
Option D The overlapping fragments from are query sequence are fed into different
kernels (similar to nodes)

QUESTION 5 Which of the following is incorrect regarding Eponine?

Option A It is a web-based program that predicts transcription start sites
Option B It is based on a series of pre-constructed PSSMs of several regulatory sites

Option C The regulatory sites include the TATA box, the CCAAT box, and CpG islands
Option D It is a web-based program that particularly predicts tranposons and retroposons

QUESTION 6 Accurate prediction of _____ bonds may also help to predict the ____
dimensional structure of the protein of interest.
Option A nitrogen, two
Option B nitrogen, three
Option C disulfide, three
Option D oxygen, three

QUESTION 7 Which of the following is incorrect regarding First EF?

Option A It is a program that predicts promoters for bacterial DNA
Option B It is a web-based program that predicts promoters for human DNA
Option C It stands for First Exon Finder
Option D It integrates gene prediction with promoter prediction

QUESTION 8 The input for the neural network includes parameters for sequence physical
properties, such as ______
Option A DNA bendability
Option B Signals such as the TATA box
Option C Signals such as initiator box
Option D Signals such as CpAA islands

QUESTION 9 Which of the following is incorrect regarding CONPRO?

Option A It is a web-based program that uses a consensus method
Option B It is used to identify promoter elements for human DNA
Option C cDNA does not play a role in prediction
Option D The program uses the information to search the human genome database for the
position of the gene

QUESTION 10 The ______ is an ongoing community-wide experiment on the comparative

evaluation of protein-protein docking for structure prediction.
Option A Chronological Assignment of Prediction of Interactions (CAPRI)
Option B Chronological Assessment of Prediction of Interactions (CAPRI)
Option C Chronological Assessment of Prediction of Interactions (CAPRI)
Option D Critical Assessment of Prediction of Interactions (CAPRI)

QUESTION 11 Which of the following is incorrect regarding FindTerm?

Option A It is a program for searching bacterial ρ-independent termination signals located
at the end of operons
Option B It is a program for searching bacterial ρ-dependent termination signals located
within the operons
Option C The predictions are made based on matching of known profiles of the
termination signals combined with energy calculations
Option D It is available from the same site as FGENES and BPROM

QUESTION 12 A disulfide bridge is a unique type of _____ modification in which _____ bonds
are formed between cysteine residues.
Option A posttranslational, covalent
Option B translational, covalent
Option C translational, ionic
Option D posttranslational, ionic
Option D They tend to have a very high gene density
QUESTION 13 Which of the following is untrue about Ab Initio–Based Programs for Gene
Prediction?
Option A The goal of the ab initio gene prediction programs is to discriminate exons from
noncoding sequences
Option B The goal is joining exons together in the correct order
Option C The main difficulty is correct identification of exons
Option D To predict exons, the algorithms rely solely on gene signals

QUESTION 14 Most vertebrate genes use __________ as the translation start codon and have a
uniquely conserved flanking sequence call a Kozak sequence (CCGCCATGG).
Option A AAG
Option B ATG
Option C AUG
Option D AGG

QUESTION 15 Which of the following is untrue about Prediction Using Neural Networks for
Gene Prediction?
Option A A neural network is a statistical model with a special architecture for pattern
recognition and classification
Option B It is composed of a network of mathematical variables
Option C They resembles ab initio approaches
Option D The variables in NeuralNetworks resemble the biological nervous system, with
variables or nodes connected by weighted functions that are analogous to
synapses

QUESTION 16 In a statistical learning process called support vector machine (SVM), a

hyperplane is _____
Option A a linear or nonlinear mathematical function
Option B nonlinear mathematical function
Option C linear mathematical function
Option D exponential mathematical function

QUESTION 17 Which of the following is untrue regarding the drawbacks of expressed sequence
tags (ESTs)?
Option A They are often of lowquality because they are automatically generated without
verification
Option B Many bases are ambiguously determined, represented by N’s
Option C Frame shift errors and artifactual stop codons are some common errors
Option D Despite of all the failures, the translation the sequences is smooth

QUESTION 18 To improve the specificity of prediction, some algorithms selectively ______

coding regions and focus on the upstream regions________ which are most
likely to contain promoters. In that sense, promoter prediction and gene
prediction are coupled.
Option A exclude, (0.5 to 2.0 kb) only
Option B include, (0.5 to 2.0 Mb) only
Option C exclude, (0.5 to 2.0 Mb) only
Option D include, (0.5 to 2.0 kb) only

QUESTION 19 Which of the following is untrue about translation and transcription?

Option A The first is capping is at the 5’ end of the transcript which involves methylation
at the initial residue of the RNA
Option B The splicing process involves a large RNA-protein complex called spliceosome
Option C The second event is splicing, which is the process of removing exons and joining
 introns
Option D The second event is splicing, which is the process of removing introns and
joining exons

QUESTION 20 Which of the following is a wrong statement?

Option A To assume biological activity, many nascent polypeptides have to be covalently
modified before or after the folding process
Option B In eukaryotic cells most modifications take place in the endoplasmic reticulum
and the Golgi apparatus
Option C The modifications in eukaryotic cells include proteolytic cleavage; formation of
disulfide bonds; addition of phosphoryl, methyl, acetyl, or other groups onto
certain amino acid residues
Option D The modifications in eukaryotic cells doesn’t include attachment of
oligosaccharides or prosthetic groups to create mature proteins

QUESTION 21 Once an operon structure is known ______ for the presence of a promoter and
regulatory elements _____ in the operon do not possess such DNA elements.
Option A only the first gene is predicted, whereas other genes
Option B only the first hundred genes are predicted, whereas next few genes
Option C only first two genes are predicted, whereas next few genes
Option D only first ten genes are predicted, whereas next few genes

QUESTION 22 Which of the following is untrue regarding expressed sequence tags (ESTs)?
Option A One of the high throughput approaches to genome-wide profiling of gene
expression is sequencing ESTs
Option B They are short sequences obtained from cDNA clones
Option C They serve as short identifiers of full-length genes
Option D They are typically in the range of 800 to 900 nucleotides in length

QUESTION 23 RNA structures can be experimentally determined using _____

Option A X-ray crystallography techniques only
Option B NMR techniques only
Option C X-ray crystallography or NMR techniques
Option D Gel electrophoresis

QUESTION 24 Which of the following is untrue about FGENES?

Option A It stands for FindGenes
Option B It is a web-based program that uses LDA
Option C It is used to determine whether a signal is an exon
Option D It does not make a use of HMMs

QUESTION 25 The ______ refers to a structure with two ends of a single-stranded region (loop)
connecting a base-paired region (stem).
Option A helical junctions
Option B hairpin loop
Option C bulge loop
Option D interior loop

QUESTION 26 Which of the following is untrue about EST2Genome?

Option A It is a web-based program purely based on the sequence alignment approach to
 define intron–exon boundaries
Option B It compares an EST (or cDNA) sequence with a genomic DNA sequence
containing the corresponding gene
Option C The alignment is rarely done using a dynamic programming–based algorithm
Option D Advantage of the approach is the ability to find very small exons and
alternatively spliced exons that are very difficult to predict by any ab initio–type
algorithms

QUESTION 27 The __________ refers to two single-stranded regions on opposite strands

connecting two adjacent base-paired segments.
Option A hairpin loop
Option B interior loop
Option C pseudoknot loop
Option D helical junctions

QUESTION 28 Which of the following is untrue about SGP-1?

Option A The program translates all potential exons in each sequence and does pair wise
alignment for the translated protein sequences using a dynamic programming
approach
Option B The near-perfect matches at the protein level define coding regions
Option C It is a similarity-based web program that aligns two genomic DNA sequences
from distinctly related organisms
Option D It stands for Syntenic Gene Prediction

QUESTION 29 In addition to the canonical base pairing, there often exists non-canonical base
pairing such as _________ and ________ base paring.
Option A G, U
Option B U, U
Option C G, A
Option D A, A

QUESTION 30 Which of the following is untrue about Prediction Using Neural Networks for
Gene Prediction?
Option A A neural network is constructed with multiple layers; the input, output, and
hidden layers
Option B The input is the gene sequence with intron and exon signals
Option C The model is not fed with a sequence of known gene structure
Option D The output is the probability of an exon structure

QUESTION 31 Ab initio approach makes structural predictions based on ______

Option A a single RNA sequence
Option B comparing RNA sequences
Option C evolutionary basis
Option D pure phylogenetics

QUESTION 32 Which of the following is untrue about Prediction Using Discriminant Analysis
for Gene Prediction?
Option A QDA draws a curved line based on a quadratic function
Option B LDA works by drawing a diagonal line that best separates coding signals from
noncoding signals based on knowledge learned from training data sets of known
 gene structures
Option C Some gene prediction algorithms rely on discriminant analysis, either LDA or
quadratic discriminant analysis (QDA), to improve accuracy
Option D LDA works by plotting a three-dimensional graph of coding signals versus all
potential 3’ splice site positions

QUESTION 33 In ab initio approach, generally, when a base pairing is formed, the energy of the
molecule is _________ because of attractive interactions between the two
strands.
Option A increased
Option B lowered
Option C multiplied
Option D kept stable

QUESTION 34 Which of the following is untrue about Homology-Based Programs?

Option A They are based on the fact that exon structures and exon sequences of related
species are less conserved
Option B This approach assumes that the database sequences are correct
Option C It is a reasonable assumption in light of the fact that many homologous
sequences to be compared with are derived from cDNA or expressed sequence
tags (ESTs) of the same species
Option D Potential coding frames in a query sequence are translated and used to align with
closest protein homologs found in databases

QUESTION 35 The attractive interactions lead to _________ energy.

Option A increased
Option B higher
Option C lower
Option D no change in

QUESTION 36 Which of the following is incorrect regarding BPROM?

Option A It is a web-based program for prediction of bacterial promoters
Option B It is a web-based program only for prediction of eukarotic promoters
Option C It uses a linear discriminant function
Option D The linear discriminant function is combined with signal and content
information

QUESTION 37 If the base pair is adjacent to loops or bulges, the neighboring loops and bulges
tend to ___________ the base-pair formation.
Option A have no change on
Option B decrease the energy
Option C stabilize
Option D destabilize

QUESTION 38 Which of the following is correct regarding the method for prokaryotic operon
prediction?
Option A It relies on two kinds of information: gene orientation and intergenic distances of
a pair of genes of interest and conserved linkage of the genes based on
comparative genomic analysis
Option B It relies only on the gene orientation and intergenic distances of a pair of genes
of interest
Option C It relies only on the conserved linkage of the genes based on comparative
genomic analysis
Option D The prediction cannot be done manually using the rules

QUESTION 39 ___________ of covariation can be ___________ to the RNA structure and

functions.
Option A Any inadequacy, advantageous
Option B Any abundance, deleterious
Option C Any lack, benign
Option D Any lack, deleterious

QUESTION 40 Which of the following is incorrect regarding the Prediction for Eukaryotes?
Option A The consensus patterns are only derived from bioinformatics studies
Option B The experimentally determined DNA binding sites are compiled into profiles
and stored in a database for scanning an unknown sequence to find similar
conserved patterns
Option C The consensus patterns are derived from experimentally determined DNA
binding sites
Option D The ab initio method for predicting eukaryotic promoters and regulatory
elements relies on searching the input sequences for matching of consensus
patterns of known promoters and regulatory elements