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For searching a query sequence with a database, which of the following statement is correct?
a)
b)
c)
d)
PAM62
BLOSUM 62
BLOSUM 60
BLOSUM 80
PAM matrices are derived by noting evolutionary changes in protein sequences that are more
than:
a)
b)
c)
d)
80% similar
60% similar
40% similar
25% similar
Which alignment is used to predict whether two sequences are homologous or not?
a) Local
b) Global
c) Pair-wise
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d) Multiple
In Molecular Dynamics simulation, the dependence is on:
a)
b)
c)
d)
only position
only momentum
both position and momentum
either position or momentum
In phylogenetic analysis, maximum likelihood method is chosen when the sequences have:
a)
b)
c)
d)
strong similarity
local similarity
medium level similarity
no clear identifiable similarity
In Needleman Wunsch algorithm of pairwise alignment of sequences with lengths n and m, the
computational time is proportional to:
a)
b)
c)
d)
nxm
(n+1) x (m+1)
n+m
n x (m+1)
In a PHYLIP output, the first line is two numbers, what do they indicate?
a)
b)
c)
d)
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What is PROSITE?
a)
b)
c)
d)
Genbank
PDB
Prodom
Swissprot
OMIM
Entrez
PubMed
PROSITE
To know the structural similarity between two proteins, the server to use is
a)
b)
c)
d)
PRODOM
PROSITE
TREMBLE
DALI
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b) PDB
c) OMIM
d) HTGS
Which of the following amino acids is least mutable according to PAM scoring matrix?
a)
b)
c)
d)
Alanine
Glutamine
Methionine
Cysteine
You have two distantly related proteins. Which of the following sets is the best for comparing
them?
a)
b)
c)
d)
BLOSUM45 or PAM250
BLOSUM45 or PAM1
BLOSUM80 or PAM250
BLOSUM80 or PAM1
In a sequence database of a given size, which of the following expressions is likely to retrieve
more matches (X means any amino acid; any of the residues in square brackets can occupy
that position)?
a)
b)
c)
d)
D-A-V-I-D
[DE]-A-V-I-[DE]
[DE]-[AVILM]-X-E
D-A-V-E
Which alignment is used to predict whether two sequences are homologous or not?
a)
b)
c)
d)
Local
Global
Pair-wise
Multiple
BLOCKS refers to
a)
b)
c)
d)
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CpG islands and codon bias are tools used in eukaryotic genomics to identify open reading
frames
a)
b)
c)
d)
Neural network
Rule-based system
Hidden Markovs model
Statistics based
BLASTx is used to
a)
b)
c)
d)
Entrez
Bioedit
Vecscreen
Rasmol
position only
momentum only
both position and momentum
either position or momentum
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sequence similarity
structural similarity
both sequence and structural similarity
basic physicochemical principles
To know the structural similarity between two proteins, the server to use is
a)
b)
c)
d)
PRODOM
PROSITE
TREMBLE
DALI
Drug design
Protein modeling
Aligning two sequences
Molecular Dynamics simulation
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Arabidopsis thaliana
Fritillaria assyriaca
Zea mays
Triticum dicoccum
Conformation
Configuration
Classification
Conservation
The program used to convert raw sequence output to an ordered list of bases is called
a)
b)
c)
d)
Base calling
Neural network
Local area network
artificial network
Which of the following algorithms implements once a gap, always a gap policy?
a)
b)
c)
d)
ClustalW
Needleman & Wunsch
Chou & Fasman
FASTA
The sequence alignment tool for immunoglobulins, T-cell receptors, and HLA molecules
available at the ImMunoGeneTics information system (IMGT) is
a)
b)
c)
d)
IMGT/Collier-de-perles
IMGT/V-Quest
IMGT/Allele-align
IMGT/Junction Analysis
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102 residues
10 residues
103 residues
104 residues
Which of the following scoring matrices is one of the best to score an alignment of highly
conserved protein sequences?
a)
b)
c)
d)
Which one of the following programs is used primarily for submission of complete genomes and
batch submission of sequences to GenBank?
a)
b)
c)
d)
BankIt
Sequin
tbl2asn
WEBIN
In reconstruction of phylogenetic trees using molecular sequence data, a singleton site in MSA
is considered to be
a)
b)
c)
d)
an invariant site
an informative variable site
an uninformative variable site
a conserved site
Accession
GI
Date
Both a & b
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d) either 5 to 3 or 3 to 5
Which of the following methods is used to predict the 3D structure of a protein when it has <
20% of sequence similarity with the available templates?
a)
b)
c)
d)
Homology modelling
Dynamic programming
Fold recognition
Progressive protein programming
Which one of the following techniques is used for the evaluation of phylogenetic trees?
a)
b)
c)
d)
Null hypothesis
Bootstrapping
Chi-square
Probability
NiceProt is
a)
b)
c)
d)
TBLASTX matches a DNA query sequence, translated into all six reading frames, against a
DNA database with
a)
b)
c)
d)
No gaps allowed
Gaps allowed
Gaps depending on the input sequence
Gaps depending on the database
Changing which of the following BLAST parameters would tend to yield fewer search results?
a) Turning off the low complexity filter
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Which information among the following provides the maximum information to do structure based
drug design?
a)
b)
c)
d)
Stick
Ball and stick
Ribbon
CPK/space filling
Hemoglobin, myoglobin and globin v protein sequences will be stored in PIR-PSD database as
a
a)
b)
c)
d)
Sub-family
Superfamily
Group
GenPept
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The biggest problem in predicting protein coding genes from genome sequencing algorithm is
that
a)
b)
c)
d)
Artificial intelligence technique is used to predict secondary structure of globular protein. Which
of the following methods uses this technique to predict secondary structures of globular
proteins?
a)
b)
c)
d)
NCBI
EMBL
EBI
RCSB
National Center for Biotechnology Information (NCBI) was established on November 4, 1988 as
a division of the
a)
b)
c)
d)
scoring a matrix
setting up a matrix
local alignment
identifying the optimal alignment
RCSB is
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To identify the presence of repeats in a protein, the simplest and fastest way is to perform a
a)
b)
c)
d)
self dot-plot
dot-plot with another protein with same repeats
dot-plot with another protein with any repeat
BLAST search
Which one of the following best represents the central dogma of Bioinformatics?
a)
b)
c)
d)
Sequence-Structure-Function
DNA-RNA-Proteins
Motifs-domains-Superfamilies
Data-Databanks-Data mining tools
Motifs
Primers
PSSMs
HMMs
Which one of the following matrices can be used to identify distantly related homologs?
a)
b)
c)
d)
BLOSUM90
BLOSUM62
BLOSUM45
BLOSUM80
Identification of MUMs
Sorting of MUMs
Alignment of MUMs
Tabulating MUMs
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a) Needleman & Wunsch algorithm is used for global alignment of pair of sequences.
b) There could be several possible local alignments as part of a global alignment.
c) In Needleman & Wunsch algorithm sequences are randomised by keeping length and
composition same.
d) The terms identity, similarity and homology are expressed as %.
Maximum parsimony analysis in the context of molecular phylogeny implies
a)
b)
c)
d)
In protein sequence analysis, Twilight zone refers to the evolutionary distance corresponding to
about
a)
b)
c)
d)
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Which one of the following proteins can be used as a template for structure prediction by
homology modelling?
a)
b)
c)
d)
1
2
3
4
Which of the following descriptors would be a suitable set for QSAR analysis?
a) logP, molecular volume, Hammet and constants, molar refractivity, polar
surface area
b) logP, number of synthetic steps, polar surface area, molar refractivity
c) logP, number of nitrogen atoms, Hammet and constants, molar refractivity, polar
surface area
d) molecular weight, molecular volume, molecular surface area.
PAM120, PAM80 and PAM60 scoring matrices are most suitable for aligning sequences with
a)
b)
c)
d)
A protein has three domains P, Q, and R, whereas another protein has three domains R, S and
Q in that order. The preferred alignment algorithm for these two proteins will be
a)
b)
c)
d)
Local alignment
Global alignment
Both algorithms will give the same results
None of the methods are suitable in this case
When p and q are lengths of sequences, the computational complexity of the Needleman and
Wunsch algorithm is
a)
b)
c)
d)
O(pq)
O(p+q)
O (q log p)
O (pq)
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You are interested in a particular enzyme that is expressed in various human tissues. You have
isolated the protein from the brain, liver and kidneys. After a lot of experimentation you
determine that the liver protein has three domains A, B and C occurring in sequential order.
Domain B is the catalytic domain and the other two have regulatory function. The kidney protein
has only domains A and B in that order and the brain protein has domains B and C. You then
proceed to determine the primary structure of the proteins using chemical methods and find that
the amino acid sequence of the three domains are completely identical regardless of the source
from which they were isolated. You then ask the question whether the three different proteins
have all originated from the same gene by means of alternative splicing, or they could be
products of different genes. Having the experimentally determined protein sequences and
knowing the sequence of the human genome, which one of the following bioinformatic method
you will use to answer the question above.
a) TBLASTN using the protein sequence as query and the human genome sequence
as database.
b) TBLASTX using the protein sequence as query and the human genome sequence as
database.
c) BLASTN using the protein sequence as query and the human genome sequence as
reference.
d) BLASTP using the protein sequence as query and the human genome sequence as
reference.
Which of the following terms will have to be taken into consideration for developing a potential
function for docking simulation?
a)
b)
c)
d)
References
DBT-JRF Question papers and Answer Keys
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