For the 10-residue DNA sequence example, there are _______ possible starting sites for a 20-residue-long site.
1.70
2.51
3.81
4.40
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.
1. energy-based
2.residue-based
3. structure-based
4.sequence-based
A transgenic crop of the future, golden rice has which of the following improved traits?
1.High lysine (essential amino acid) content
2.Insect resistance
3.High protein content
4.High vitamin-A content
Approximately how many varieties of rice are there in India?
1.2,000
2.20,000
3.200,000
4.2,000,000
In Genetic Algorithm, in the mutation process _____
1.sequence is not changed
2. sequence is changed
3.gaps are not rearranged
4. gaps are not inserted
The cultivation of Bt cotton has been much in the news. Bt stands for
1. barium-treated cotton seeds
2.bigger thread variety of cotton with better tensile strength
3.produced by biotechnology using restriction enzymes and ligases
4. carrying an endotoxin gene from Bacillus thuringiensis
The initial alignments used to produce the guide tree may be obtained by various methods. Which of the following is not one of them?
1. pattern-finding approach similar
2.FASTA
3. Faster, full dynamic programming method
4. Fast k-tuple
What is a tumour-inducing plasmid widely used in producing transgenic plants?
1.Escherichia coli
2.Bacillus thuringiensis
3.Staphylococcus aureus
4.Agrobacterium tumefaciens
What is the process by which crop plants are enriched with certain desirable nutrients?
1. crop protection
2.breeding
3. bio-fortification
4. bio-remediation
What is used to generate parameters for the extreme distribution?
1.The pool of alignment scores from the unshuffled sequences
2.The pool of alignment scores from the shuffled sequences
3.The basic optimal score computed at the beginning of the test
4.A single score of a shuffled sequence
Which of the following does not describe local alignment algorithm?
1.In traceback step, beginning is with the highest score, it ends when 0 is encountered
2. First row and first column are set to 0 in initialization step
3.Score can be negative
4.Negative score is set to 0
Which of the following feature of Bayesian methods is the disadvantage?
1.A specific mutational model is required
2. Computationally Bayesian methods are better
3.A length and distance that gives the highest overall probability may be determined
4.They are used to calculate evolutionary distance
Which of the following is a variety of Brassica that is resistant to white rust?
1.Himgiri
2.Pusa Kamal
3.Pusa Swarnim (Karan rai)
4.Pusa Sadabahar
Which of the following is an abbreviation of MEME?
1.Multiple Expectation Maximization for Motif Extraction
2.Mega Expectation Maximization for Motif Elicitation
3. Micro Expectation Maximization for Motif Extraction
4.Multiple Expectation Maximization for Motif Elicitation
Which of the following is an incorrect statement?
1.Molscript is not capable of generating ball-and-stick styles
2.In particular, secondary structure elements can be drawn with solid spirals and arrows representing ?-helices and ?-strands, respectively
3.Molscript is capable of generating space-filling
4.Molscript is a UNIX program capable of generating wire-frame
Which of the following is incorrect about ENTREZ?
1.It provides a series of forms that can be filled out to retrieve a Medline reference related to the molecular biology sequence databases
2.It provides a series of forms that can be filled out to retrieve a DNA or protein sequence
3.It is a resource prepared only by the staff of the National Center for Biotechnology Information
4.One straightforward way to access the sequence databases is through ENTREZ
Which of the following is incorrect regarding sequence homology?
1. It is an important concept in sequence analysis
2.When two sequences are descended from a common evolutionary origin, they are said to share homology
3. Two sequences can homologous relationship even if have do not have common origin
4.When two sequences are descended from a common evolutionary origin, they are said to have a homologous relationship
Which of the following is not a benefit of BLAST?
1.Speed
2.Statistical rigor
3.Handling of gaps
4.More sensitive
Which of the following is not a form of RNA?
1.tRNA
2.rRNA
3.mRNA
4.qRNA
Which of the following is not a site on internet for alignment of sequence pairs?
1.BLASTN
2.BCM Search Launcher
3.BLASTX
4.SIM
Which of the following is not a software for dot plot analysis?
1.DOTMATCHER
2.LALIGN
3.DOTLET
4.SIMMI
Which of the following is not a variant of BLAST?
1.BLASTX
2.TBLASTNX
3.BLASTP
4.BLASTN
Which of the following is not among the methods for finding localized sequence similarity?
1.Extraction of Blocks from a Global or Local MSA
2.Pattern blocking
3.Block Analysis
4.Profile Analysis
Which of the following is not correct about FASTA?
1.It was in fact the first database similarity search tool developed, preceding the development of BLAST
2.FASTA uses a ‘hashing’ strategy to find matches for a short stretch of identical residues with a length of k
3.The string of residues is known as blocks
4. Its stands for FAST ALL
Which of the following is not correct about the Coils and Loops?
1. They are irregular structures
2.If the connecting regions are completely irregular, they belong to random coils
3.They are regular structures
4.The loops are often characterized by sharp turns or hairpin-like structures
Which of the following is not one of the requirements for implementing algorithms for sequence database searching?
1.Speed
2. Size of the dataset
3.Sensitivity
4.Specificity
Which of the following is not the objective to perform sequence comparison?
1.To find the common motifs present in both sequences
2.To study the physical properties of molecules
3.To study evolutionary relationships
4.To observe patterns of conservation
Which of the following is true regarding Coiled coil?
1. They have an integral repeat of seven residues
2. They have an integral repeat of thirty residues
3.The sequence periodicity doesn’t contribute in designing algorithms to predict the structural domain
4. They have an integral repeat of twenty residues
Which of the following is true regarding the assumptions in the method of constructing the Dayhoff scoring matrix?
1.sites do not vary in their degree of mutability
2.it is assumed that each amino acid position is equally mutable
3.it is assumed that each amino acid position is not equally mutable
4. it is assumed that each amino acid position is not mutable at all
Which of the following is untrue about homology modeling?
1. It doesn’t involve the evolutionary distances anywhere
2.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
3. Homology modeling predicts protein structures based on sequence homology with known structures
4.It is also known as comparative modeling
Which of the following is untrue about Loop Modeling Step?
1.The gaps cannot be directly modeled
2. Loop modeling is required for closing the gaps requires
3.In the sequence alignment for modeling, there are no regions producing gaps in sequence alignment
4.In the sequence alignment for modeling, there are often regions caused by insertions and deletions producing gaps in sequence alignment
Which of the following is untrue about SCOP?
1. It is constructed almost entirely based on manual examination of protein structures
2.The SCOP families consist of proteins having low sequence identity (>30%)
3.It is a database for comparing and classifying protein structures
4.The proteins are grouped into hierarchies of classes, folds, superfamilies, and families
Which of the following is untrue about the iterative approach?
1.Because the order of the sequences used for alignment is different in each iteration
2.This method is not based on heuristic methods
3.The iterative approach is based on the idea that an optimal solution can be found by repeatedly modifying existing suboptimal solutions
4.This method is also heuristic in nature and does not have guarantees for finding the optimal alignment
Which of the following is untrue regarding Chou–Fasman and GOR methods?
1.They suffer from the fact that the prediction rules are somewhat arbitrary
2.They are based on single sequence statistics with clear relation to known protein-folding theories
3.They are developed in the 1970s
4.Both are the first-generation methods
Which of the following is untrue regarding Prediction with Neural Networks?
1.A neural network is trained by a single sequence
2.When the sufficiently trained network processes an unknown sequence, it applies the rules learned in training to recognize particular structural patterns
3.When multiple sequence alignments and neural networks are combined, the result is further improved accuracy
4.A neural network is trained by a sequence profile derived from the multiple sequence alignment
Which of the following is untrue regarding the transmembrane proteins?
1.The membrane proteins are also of tremendous biomedical importance
2. They are not drug targets or receptors
3.They are responsible for performing a wide variety of important functions in a cell, such as signal transduction, cross-membrane transport, and energy conversion
4.Constitute up to 30% of all cellular proteins
Which of the following is wrong about National Biomedical Research Foundation/Protein Information Resource Sequence Format?
1. This is different than PIR format
2. The first line includes an initial “>” character followed by a two-letter code such as P for complete sequence or F for the fragment, followed by a 1 or 2 to indicate type of sequence, then a semi
3.The NBRF format is similar to the FASTA sequence format but with significant differences
4.Sequences retrieved from the PIR database are not in this compact format, but in an expanded format with much more information about the sequence
Which of the following scores are not considered while calculating the SP scores?
1.Number of gap penalties
2. All possible pair wise matches
3.All possible mismatches
4.All possible gap costs