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1000 Bioinformatics
Quiz 2
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Q.1
Which of the following is not among the methods for finding localized sequence similarity?
a) Extraction of Blocks from a Global or Local MSA
b) Pattern blocking
c) Block Analysis
d) Profile Analysis
Q.2
For the 10-residue DNA sequence example, there are _______ possible starting sites for a 20-residue-long site.
a) 70
b) 51
c) 81
d) 40
Q.3
MACAW is a local multiple sequence alignment program and a sequence editing tool.
a) True
b) False
Q.4
Which of the following is not one of the requirements for implementing algorithms for sequence database searching?
c) Sensitivity
a) Speed
b) Size of the dataset
d) Specificity
Q.5
Which of the following is not a variant of BLAST?
a) BLASTX
b) TBLASTNX
c) BLASTP
d) BLASTN
Q.6
Which of the following is not correct about FASTA?
a) It was in fact the first database similarity search tool developed, preceding the development of BLAST
b) FASTA uses a ‘hashing’ strategy to find matches for a short stretch of identical residues with a length of k
c) The string of residues is known as blocks
d) Its stands for FAST ALL
Q.7
Which of the following is not a benefit of BLAST?
a) Speed
b) Statistical rigor
c) Handling of gaps
d) More sensitive
Q.8
Which of the following is not correct about the Coils and Loops?
a) They are irregular structures
b) If the connecting regions are completely irregular, they belong to random coils
c) They are regular structures
d) The loops are often characterized by sharp turns or hairpin-like structures
Q.9
Which of the following is an incorrect statement?
a) Molscript is not capable of generating ball-and-stick styles
b) In particular, secondary structure elements can be drawn with solid spirals and arrows representing α-helices and β-strands, respectively
c) Molscript is capable of generating space-filling
d) Molscript is a UNIX program capable of generating wire-frame
Q.10
Which of the following is untrue about SCOP?
a) It is constructed almost entirely based on manual examination of protein structures
b) The SCOP families consist of proteins having low sequence identity (>30%)
c) It is a database for comparing and classifying protein structures
d) The proteins are grouped into hierarchies of classes, folds, superfamilies, and families
Q.11
Which of the following is untrue regarding Prediction with Neural Networks?
a) A neural network is trained by a single sequence
b) When the sufficiently trained network processes an unknown sequence, it applies the rules learned in training to recognize particular structural patterns
c) When multiple sequence alignments and neural networks are combined, the result is further improved accuracy
d) A neural network is trained by a sequence profile derived from the multiple sequence alignment
Q.12
Which of the following is true regarding Coiled coil?
a) They have an integral repeat of seven residues
b) They have an integral repeat of thirty residues
c) The sequence periodicity doesn’t contribute in designing algorithms to predict the structural domain
d) They have an integral repeat of twenty residues
Q.13
Which of the following is untrue regarding Chou–Fasman and GOR methods?
a) They suffer from the fact that the prediction rules are somewhat arbitrary
b) They are based on single sequence statistics with clear relation to known protein-folding theories
c) They are developed in the 1970s
d) Both are the first-generation methods
Q.14
Which of the following is untrue about homology modeling?
a) It doesn’t involve the evolutionary distances anywhere
b) The principle behind it is that if two proteins share a high enough sequence similarity, they are likely to have very similar three-dimensional structures
c) Homology modeling predicts protein structures based on sequence homology with known structures
d) It is also known as comparative modeling
Q.15
In the pairwise energy based method, a protein sequence is searched for in a structural fold database to find the best matching structural fold using ______ criteria.
a) energy-based
b) residue-based
c) structure-based
d) sequence-based
Q.16
Which of the following is untrue about Loop Modeling Step?
a) The gaps cannot be directly modeled
b) Loop modeling is required for closing the gaps requires
c) In the sequence alignment for modeling, there are no regions producing gaps in sequence alignment
d) In the sequence alignment for modeling, there are often regions caused by insertions and deletions producing gaps in sequence alignment
Q.17
Which of the following is not a form of RNA?
a) tRNA
b) rRNA
c) mRNA
d) qRNA
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