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Multiple choice question for engineering

Set 1

1. Originally, the FOLD program of _____ predicted _____ having the minimum free energy.
a) M. Zuker, two structures
b) M. Wunsch, two structures
c) M. Zuker, only one
d) M. Wunsch, only one

View Answer

Answer: c [Reason:] However, changes in a single nucleotide can result in drastic changes in the predicted structure. A later version, called MFOLD, has improved prediction of non-base paired interactions and predicts several structures having energies close to the minimum free energy.

2. To find suboptimal structures, the dynamic programming method was modified.
a) True
b) False

View Answer

Answer: a [Reason:] it was so done to evaluate parts of a new scoring matrix in which the sequence is represented in two tandem copies on both the vertical and horizontal axes. The regions from i 1 to n and j 1 to n are used to calculate an energy V (i,j) for the best structure that includes an i,j base pair and is called the included region.

3. In the programs related to FOLD, the second region, the ______ region, is used to calculate the energy of the ____ structure.
a) included, most likely
b) included, best
c) excluded, least likely
d) excluded, best

View Answer

Answer: d [Reason:] A second region, the excluded region, is used to calculate the energy of the best structure that includes i,j but is not derived from the structure at i+1, j-1 After certain corrections are made, the difference between the included and excluded values is the most energetic structure that includes the base pair i, j.

4. In the programs related to FOLD, All complementary base pairs can be sampled in a fashion to determine which are present in a suboptimal structure.
a) True
b) False

View Answer

Answer: [Reason:] All complementary base pairs can be sampled in a fashion to determine which are within a certain range of the optimal one. An energy dot plot is produced showing the locations of alternative base pairs that produce the most stable or suboptimally stable structures.

5. The program may be instructed to find structures within a certain percentage of the minimum free energy.
a) True
b) False

View Answer

Answer: a [Reason:] Parameter d provides a measure of similarity between two structures. When MFOLD is established on a suitable local host machine, the window is interactive, and clicking a part of the display will lead to program output of the corresponding structure.

6. Three scores, Pnum (i), Hnum (i,j), and Ssum, have been derived to assist with a determination of the reliability of a secondary structure prediction for a particular base i or a base pair i,j.
Pnum ____
Which of the following is not a correct blank?
a) is the total number of energy dots regardless of color in the i th row and i th column of the energy dot plot
b) is the total number of energy dots considering the color in the ith row and ith column of the energy dot plot
c) represents in an unfiltered dot plot
d) represents the number of base pairs

View Answer

Answer: b [Reason:] it represents the number of base pairs that the ith base can form with all other base pairs in structures within the defined energy range. The lower this value, the better defined or “well determined” the local structure because there are few competitive foldings.

7. Three scores, Pnum (i), Hnum (i,j), and Ssum, have been derived to assist with a determination of the reliability of a secondary structure prediction for a particular base i or a base pair i,j.
Hnum ____
Which of the following is not a correct blank?
a) is the sum of Pnum(i) and Pnum(j) -1
b) is the sum of Pnum(i) and Pnum(j) + 1
c) is the total number of dots in the ith row and jth column
d) represents the total number of base pairs with the ith or jth base in the predicted structures

View Answer

Answer: b [Reason:] The Hnum for a double stranded region is the average Hnum value for the base pairs in that helix. The lower this number, the more well determined the double-stranded region.

8. Three scores, Pnum (i), Hnum (i,j), and Ssum, have been derived to assist with a determination of the reliability of a secondary structure prediction for a particular base i or a base pair i,j.
Ssum ____
Which of the following is not a correct blank?
a) is also called as ss-count
b) is the number of foldings in which base i is single-stranded divided by m, the number of folding
c) is the number of foldings in which base i is single-stranded multiplied by m, the number of folding
d) gives the probability that base i is single-stranded

View Answer

Answer: c [Reason:] If Snum is approximately 1, then base i is probably in a single-stranded region, and if Snum is approximately 0, then base i is probably not in such a region. This reliability information has been used to annotate output files of MFOLD and other RNA display programs.

9. A limitation of the Zuker method and other methods (Nakaya et al. 1995) for computing suboptimal RNA structures is that they do not compute all the structures within a given energy range of the minimum free-energy structure.
a) True
b) False

View Answer

Answer: a [Reason:] For example, no alternative structures are produced that have the absence of base pairs in the best structure, and, if two substructures are joined by a stretch of unpaired bases, no structures are produced that are suboptimal for both structures. These factors limit the number of alternative structures predicted compared to known variations based on sequence variations in tRNAs.

10. These limitations of the Zuker method and other methods have been largely overcome by using an algorithm originally described by Waterman and Byers (1985) for finding sequence alignments within a certain range of the optimal one by modifications of the trace-back procedure used in dynamic programming.
a) True
b) False

View Answer

Answer: a [Reason:] This method efficiently calculates a large number of alternative structures, up to a very large number, within a given energy range of the minimum free-energy structure. The method has been used to demonstrate that natural tRNA sequences can form many alternative structures which are close to the minimum free-energy structure and that base modification plays a major role in this energetic stability.

Set 2

1. Which of the following is incorrect about a microarray?
a) It is a slide attached with a high-density array of immobilized DNA oligomers representing the entire genome of the species under study
b) Array of immobilized DNA oligomers cannot be cDNAs
c) Each oligomer is spotted on the slide and serves as a probe for binding to a unique complementary cDNA
d) It is the most commonly used global gene expression profiling method

View Answer

Answer: b [Reason:] The entire cDNA population, labeled with fluorescent dyes or radioisotopes, is allowed to hybridize with the oligo probes on the chip. The amount of fluorescent or radiolabels at each spot position reflects the amount of corresponding mRNA in the cell. Using this analysis, patterns of global gene expression in a cell can be examined.

2. which of the following is incorrect about Oligonucleotide Design in A microarray?
a) DNA microarrays are generated by fixing oligonucleotides onto a solid support
b) The oligonucleotide array slide represents thousands of preselected genes from an organism
c) The length of oligonucleotides is typically in the range of twenty-five to seventy bases long
d) The oligonucleotides don’t react with cDNA samples

View Answer

Answer: d [Reason:] The oligonucleotides are called probes that hybridize to labeled cDNA samples. Shorter oligo probes tend to be more specific in hybridization because they are better at discriminating perfect complementary sequences fromsequences containing mismatches. However, longer oligos can be more sensitive in binding cDNAs.

3. Which of the following is incorrect about Data Collection?
a) The two-color microarray uses multiple dyes at times
b) The most common type of microarray protocol is the two-color microarray
c) The cDNAs are obtained by extracting total RNA or mRNA from tissues or cells and incorporating fluorescent dyes in the DNA strands during the cDNA biosynthesis
d) The expression of genes is measured via the signals from cDNAs hybridizing with the specific oligonucleotide probes on the microarray

View Answer

Answer: a [Reason:] The most common type of microarray protocol is the two-color microarray, which involves labeling one set of cDNA from an experimental condition with one dye (Cy5, red fluorescence) and another set of cDNA from a reference condition (the controls) with another dye (Cy3, green fluorescence). When the two differently labeled cDNA samples are mixed in equal quantity and allowed to hybridize with the DNA probes on the chips, gene expression patterns of both samples can be measured simultaneously.

4. In the analysis of microarray data–If replicated datasets are available, rigorous statistical tests such as t-test and analysis of variance (ANOVA) can be performed to test the null hypothesis that a given data point is not significantly different from the mean of the data distribution.
a) True
b) False

View Answer

Answer: a [Reason:] For such tests, it is common to use a P-value cutoff of .05, which means a confidence level of 95% to distinguish the data groups. This level also corresponds to a gene expression level with two standard deviations from the mean of distribution.

5. Which of the following is incorrect about Classification of microarray data?
a) For microarray data, clustering analysis identifies coexpressed and coregulated genes
b) For microarray data, clustering analysis identifies coexpressed but not coregulated genes
c) For microarray data, clustering analysis identifies and coregulated but not coexpressed genes
d) Genes within a category have more similarity in expression than genes from different categories.

View Answer

Answer: a [Reason:] When genes are co-regulated, they normally reflect related functionality. Through gene clustering, functions of previously uncharacterized genes may be discovered. Clustering methods include hierarchical clustering and partitioning clustering (e.g., k-means, self-organizing maps [SOMs]).

6. A supervised analysis refers to classification of data into a set of predefined categories. For example, depending on the purpose of the experiment, the data can be classified into predefined ‘diseased’ or ‘normal’ categories.
a) True
b) False

View Answer

Answer: a [Reason:] Similarly, an unsupervised analysis does not assume predefined categories, but identifies data categories according to actual similarity patterns. The unsupervised analysis is also called clustering, which is to group patterns into clusters of genes with correlated profiles.

7. Which of the following is incorrect about Hierarchical Clustering?
a) The tree-branching pattern illustrates a higher degree of relationship between related gene groups
b) It is not similar to the distance phylogenetic tree-building method
c) It produces a treelike structure that represents a hierarchy or relative relatedness of data groups
d) In the tree leaves, similar gene expression profiles are placed more closely together than dissimilar gene expression profiles

View Answer

Answer: b [Reason:] A hierarchical clustering method is in principle similar to the distance phylogenetic tree-building method. When genes with similar expression profiles are grouped in such a way, functions for unknown genes can often be inferred. Hierarchical clustering uses the agglomerative approach that works in much the same way as the UPGMA method, in which the most similar data pairs are joined first to form a cluster.

8. Which of the following is incorrect about k-Means Clustering?
a) k-means clustering produces a dendrogram
b) It classifies data through a single step partition
c) It is a divisive approach
d) In this method, data are partitioned into k-clusters, which are prespecified at the outset

View Answer

Answer: a [Reason:] In contrast to hierarchical clustering algorithms, k-means clustering does not produce a dendrogram, but instead classifies data through a single step partition. The value of k is normally randomly set but can be adjusted if results are found to be unsatisfactory.

9. Which of the following is incorrect about Self-Organizing Maps?
a) Clustering by SOMs is in principle similar to the k-means method
b) It doesn’t involve neural networks
c) The data points are initially assigned to the nodes at random
d) It starts by defining a number of nodes

View Answer

Answer: b [Reason:] This pattern recognition algorithm employs neural networks. The distance between the input data points and the centroids are calculated. The data points are successively adjusted among the nodes, and their distances to the centroids are recalculated. After many iterations, a stabilized clustering pattern are reached with the minimum distances of the data points to the centroids. The differences between SOM and k-means are that, in SOM, the nodes are not treated as isolated entities, but as connected to other nodes.

10. TIGR TM4 is a suite of multiplatform programs for analyzing microarray data.
a) True
b) False

View Answer

Answer: a [Reason:] This comprehensive package includes four interlinked programs, TIGR spot finder (for image analysis), MIDAS (for data normalization), MeV (for clustering analysis and visualization), and MADAM (for data management). The package provides different data normalization schemes and clustering options. Other Similar Clustering Programs are EPCLUST, SOTA.

Set 3

1. Which of the following is untrue about Amino acid conservation?
a) It has been known for some time that conservation of residues at the surface of a protein family is often related to function
b) Conservation of residues at the core of a protein family is often related to function
c) This may be an enzyme active-site or binding site
d) Unlike hydrophobicity or electrostatic potential, displaying residue conservation on the molecular surface has no physical or chemical basis

View Answer

Answer: b [Reason:] However, the evolutionary information can sometimes delineate a functional epitope allowing residues to be identified that are important for binding. In order to infer structure-function relationships the proteins must be structurally related, preferably a large family of proteins with related function.

2. Which of the following is untrue about Shape Complementarity?
a) The complementarity between two proteins or a protein and ligand can be described by surface contact or overlap
b) The complementarity between two proteins or a protein and ligand can be described by the overall buried surface area of two molecules in contact
c) The complementarity between two proteins or a protein and ligand can be described by the number of adjacent surface points (atoms or residues)
d) The hydrophobic effect barely has impact on protein folding

View Answer

Answer: d [Reason:] For example simple atom neighbor counting and the simple surface contact scores are of this type. Whilst these measures are easily calculated they also have some physical basis for being effective scoring functions. The principal driving force for protein folding and binding is the hydrophobic effect, which involves the free energy gain of removing non-polar surface area from water.

3. The burial of surface area (or the maximization of surface contact) is an approximation of the effect of shape complementarity.
a) True
b) False

View Answer

Answer: a [Reason:] However, since no distinction is generally made between polar and non-polar surface area this is an approximation. As burial of the former is unfavorable or neutral the sentence is held true.

4. Which of the following is untrue about Grid Representation?
a) To speed up the matching process the topology of the protein can be simplified from atomic level detail to a series of cubic elements
b) To speed up the matching process discretizing the 3-dimensional space using a grid is done
c) Discretizing allows very fast computer matching using search methods such as Fourier transform
d) Fourier transform is hardly used in computer matching

View Answer

Answer: d [Reason:] The shape of a molecule is described by mapping it to a 3-D grid of uniformly spaced points. Clearly the level of detail is controlled by the grid spacing. The larger the grid spacing the cruder the representation with respect to the atomic level.

5. In Grid representation, in a translational scan the mobile molecule B moves through the grid representing the static molecule A and a signal describing shape complementarity, fc, is generated for each mapping. Mathematically the correlation function, fc, of fA and fB is given by ______ where N is the number of grid points along the cubic axes i, j, and k and α, β, and γ are the translational vectors of the mobile molecule B relative to the static one A.

bioinformatics-questions-answers-molecular-complementarity-q5

View Answer

Answer: a [Reason:] The overlap between points representing the surface of the molecules is scored favorably, however, overlap with points representing the core of the static molecule are scored unfavorably. Zero correlation score is given to two molecules not in contact. Negative scores represent surface overlap with the core region of molecule A.

6. In Grid representation, the lowest score represents the best surface complementarity for a given translational scan.
a) True
b) False

View Answer

Answer: b [Reason:] The highest score represents the best surface complementarity for a given translational scan. Note that the mobile molecule must be mapped differently to the grid for each rotational change applied to the molecule.

7. In Property-based measures, displaying physical properties on the molecular surface of molecules can help to guide molecular docking.
a) True
b) False

View Answer

Answer: a [Reason:] Indeed in many cases, displaying physical properties on the molecular surface of molecules can help to guide molecular docking. Alternatively sequence conservation might also help, particularly where a homologous family of proteins maintain a specific binding partner.

8. Which of the following is untrue about Hydrophobicity?
a) The hydrophobic effect plays a dominant role in the folding of proteins
b) Hydrophobic residues aggregate away from contact with water
c) Hydrophobic residues aggregate to form hydrophobic cores with more polar residues
d) Hydrophobic residues form the solvent accessible surface but restrict the solubility of the protein

View Answer

Answer: d [Reason:] Clearly a hydrophobic interface will drive the formation of protein-protein or protein-ligand interactions. It has been noted that hydrophobicity is fairly common at protein-protein interfaces particularly in homodimers (two identical protein monomers that associate) and oligomeric proteins.

9. Oligomers are often obligate complexes meaning that the free-energy cost of dissociation is high and they exist as oligomers under physiological conditions.
a) True
b) False

View Answer

Answer: a [Reason:] In some cases biological function is dependent on this. However, many protein interactions are non-obligatory being made/broken according to their environment. These proteins must be independently stable in solution. These are commonly heterodimeric complexes including enzyme inhibitor and antibody-antigen complexes as well as a host of other casual interacting proteins. The hydrophobic effect is often much less dominant and interfaces are more polar in nature partly because of issues relating to protein stability and aggregation. Therefore, hydrophobicity is useful as a guide to molecular complementarity in selective protein-protein interactions.

10. Which of the following is untrue about Electrostatic Complementarity?
a) The electrostatic properties of biomolecules play an important role in determining interactions.
b) The burial of charged residues at protein-protein/DNA interfaces is thought to be generally net destabilizing with the hydrophobic effect being the primary driving force
c) Charged groups involved in the biomolecular interface are often stabilized by other polar or oppositely charged groups on the interacting molecule
d) Charged groups involved in the biomolecular interface are often stabilized by similar polar or same charged groups on the interacting molecule

View Answer

Answer: d [Reason:] Therefore charge complementarity can play an important role in determining the specificity of the interaction. In many cases in biology a protein must recognize a highly charged molecule such as poly-anions like DNA or RNA. In order to make a close approach the protein must have charged residues that complement the negative charges present on the phosphate backbone. Electrostatic complementarity is also important in many protein-protein and protein-ligand interactions.

Set 4

1. Which of the following is not the objective to perform sequence comparison?
a) To observe patterns of conservation
b) To find the common motifs present in both sequences
c) To study the physical properties of molecules
d) To study evolutionary relationships

View Answer

Answer: c [Reason:] To assess whether it is likely that two sequences evolved from the same sequence comparison is required. Also, to find out which sequences from the database are similar to the sequence at hand, sequence comparison is carried out.

2. A dotplot is visual and qualitative technique whereas the sequence alignment is exact and quantitative measure of similarity of alignments.
a) True
b) False

View Answer

Answer: a [Reason:] The sequence alignment is exact and quantitative measure of similarity of alignments. It involves– Construction of the best alignment between the sequences and assessment of the similarity from the alignment.

3. The global sequence alignment is suitable when the two sequences are of dissimilar length, with a negligible degree of similarity throughout.
a) True
b) False

View Answer

Answer: b [Reason:] The global sequence alignment is suitable when the two sequences are of similar length, with a significant degree of similarity throughout. It gives the best alignment over the entire length of two sequences.

4. The alignment score is the sum of substitution scores and gap penalties in this type of algorithm.
a) True
b) False

View Answer

Answer: a [Reason:] Use of +1 as a reward for a match, -1 as the penalty for a mismatch, and ignoring gaps is the scoring scheme of this type of method. Hence, the alignment score is the sum of substitution scores and gap penalties in this type of algorithm.

5. The substitution matrices are rarely used in this type of matching.
a) True
b) False

View Answer

Answer: b [Reason:] The substitution matrices are quite commonly used in this type of matching. A concise way to express the residue substitution costs can be achieved with a N x N matrix where, N is 4 for DNA and 20 for proteins as 4 nucleotides in DNA and 20 amino acid residues in proteins are in picture respectively.

6. Which of the following is untrue about Protein substitution matrices?
a) They are significantly more complex than DNA scoring matrices
b) They have the N x N matrices of the amino acids
c) Protein substitution matrices have quite important role in evolutionary studies
d) They are significantly quite less complex than DNA scoring matrices

View Answer

Answer: d [Reason:] Protein substitution matrices are significantly more complex than DNA scoring matrices. Proteins are composed of twenty amino acids, and physico-chemical properties of individual amino acids vary considerably. A protein substitution matrix can be based on any property of amino acids: size, polarity, charge, hydrophobicity.

7. In Needleman-Wunsch algorithm, the gaps are scored -2.
a) True
b) False

View Answer

Answer: b [Reason:] In Needleman-Wunsch algorithm, the gaps are ignored. Amount of gap penalty is zero here. A gap corresponds to an insertion or a deletion of a Residue.

8. The number of possible global alignments between two sequences of length N is _____
bioinformatics-questions-answers-needleman-wunsch-algorithm-q8

View Answer

Answer: b [Reason:] By the total number of permutations and combinations option b gives the accurate number of possible global alignments between two sequences of length N. For two sequences of 250 residues this is 10149.

9. Which of the following is untrue about Needleman-Wunsch algorithm?
a) It is an example of dynamic programming
b) Basic idea here is to build up the best alignment by using optimal alignments of larger subsequences
c) It was first used by Saul Needleman and Christian Wunsch
d) It was first used in 1970

View Answer

Answer: b [Reason:] In case of Needleman-Wunsch algorithm, the basic idea here is to build up the best alignment by using optimal alignments of smaller subsequences. It is based on dynamic programming, a discipline invented by Richard Bellman in 1953.

10. There are two types matrices involved in the study- score matrices and trace matrices.
a) True
b) False

View Answer

Answer: a [Reason:] The Needleman-Wunsch algorithm consists of three steps where these matrices play their role as follows: 1. Initialization of the score matrix 2. Calculation of scores and filling the traceback matrix 3. Deducing the alignment from the traceback matrix

Set 5

1. The formation of _____ is determined by ______ interactions, whereas the formation of ____ is strongly influenced by ______ interactions.
a) α-helices, long -range, α-helices, short -range
b) α-helices, long -range, β-strands, short -range
c) α-helices, short-range, β-strands, long-range
d) β-strands, short-range, β-strands, long-range

View Answer

Answer: c [Reason:] Protein secondary structure prediction with high accuracy is not a trivial ask. It remained a very difficult problem for decades. This is because protein secondary structure elements are context dependent. The formation of α-helices is determined by short-range interactions, whereas the formation of β-strands is strongly influenced by long-range interactions. Prediction for long-range interactions is theoretically difficult. After more than three decades of effort, prediction accuracies have only been improved from about 50% to about 75%.

2. The secondary structure prediction methods can be either ab initio based, which make use of single sequence information only, or homology based, which make use of multiple sequence alignment information.
a) True
b) False

View Answer

Answer: a [Reason:] The ab initio methods, which belong to early generation methods, predict secondary structures based on statistical calculations of the residues of a single query sequence. The homology-based methods do not rely on statistics of residues of a single sequence, but on common secondary structural patterns conserved among multiple homologous sequences.

3. Which of the following is untrue regarding Ab Initio–Based Methods?
a) This type of method predicts the secondary structure based on a single query sequence
b) This type of method predicts the secondary structure based on a multiple query sequence
c) It measures the relative propensity of each amino acid belonging to a certain secondary structure element
d) The propensity scores are derived from known crystal structures

View Answer

Answer: b [Reason:] Examples of ab initio prediction are the Chou–Fasman and Garnier, Osguthorpe, Robson (GOR) methods. The ab initio methods were developed in the 1970s when protein structural data were very limited. The statistics derived from the limited data sets can therefore be rather inaccurate. However, the methods are simple enough that they are often used to illustrate the basics of secondary structure prediction.

4. The Chou–Fasman algorithm determines the propensity or intrinsic tendency of each residue to be in the helix, strand, and β-turn conformation using observed frequencies found in protein crystal structures.
a) True
b) False

View Answer

Answer: a [Reason:] It determines the propensity or intrinsic tendency of each residue using observed frequencies found in protein crystal structures (conformational values for coils are not considered). For example, it is known that alanine, glutamic acid, and methionine are commonly found in α-helices, whereas glycine and proline are much less likely to be found in such structures.

5. The GOR method is based on the “propensity” of each residue to be in one of the two conformational states, helix (H), strand(E).
a) True
b) False

View Answer

Answer: b [Reason:] The GOR method is based on the “propensity” of each residue to be in one of the two conformational states, helix (H), strand(E), turn(T),and coil (C). However, instead of using the propensity value from a single residue to predict a conformational state, it takes short-range interactions of neighboring residues into account.

6. Which of the following is untrue regarding Chou–Fasman and GOR methods?
a) Both are the first-generation methods
b) They are developed in the 1970s,
c) They suffer from the fact that the prediction rules are somewhat arbitrary
d) They are based on single sequence statistics with clear relation to known protein-folding theories

View Answer

Answer: d [Reason:] They are based on single sequence statistics without clear relation to known protein-folding theories. The predictions solely rely on local sequence information and fail to take into account long range interactions. A Chou-Fasman–based prediction does not even consider the short-range environmental information.

7. Which of the following is untrue regarding Homology-Based Methods?
a) The third generation of algorithms was developed in the late 1990s
b) They were developed by making use of evolutionary information
c) This type of method uses the ab initio secondary structure prediction of individual sequences only
d) This type of method combines the ab initio secondary structure prediction of individual sequences and alignment information from multiple homologous sequences (>35% identity)

View Answer

Answer: c [Reason:] The idea behind this approach is that close protein homologs should adopt the same secondary and tertiary structure. When each individual sequence is predicted for secondary structure using a method similar to the GOR method, errors and variations may occur. However, evolutionary conservation dictates that there should be no major variations for their secondary structure elements.

8. Because residues in the same aligned position are assumed to have the same secondary structure, any inconsistencies or errors in prediction of individual sequences can be corrected using a majority rule.
a) True
b) False

View Answer

Answer: a [Reason:] By aligning multiple sequences, information of positional conservation is revealed. This homology based method has helped improve the prediction accuracy by another 10% over the second-generation methods.

9. Which of the following is untrue regarding Prediction with Neural Networks?
a) The third-generation prediction algorithms extensively apply sophisticated neural networks
b) It is used to analyze substitution patterns in multiple sequence alignments
c) It is not a machine learning process
d) It requires a structure of multiple layers of interconnected variables or nodes

View Answer

Answer: c [Reason:] a neural network is a machine learning process that requires a structure of multiple layers of interconnected variables or nodes. In secondary structure prediction, the input is an amino acid sequence and the output is the probability of a residue to adopt a particular structure.

10. Which of the following is untrue regarding Prediction with Neural Networks?
a) It has to be first trained by sequences with known structures
b) Between input and output are many connected hidden layers
c) Between the connected hidden layers the machine learning takes place to adjust the mathematical weights of internal connections
d) It doesn’t have to be first trained by sequences with known structures

View Answer

Answer: d [Reason:] The neural network has to be first trained by sequences with known structures so it can recognize the amino acid patterns and their relationships with known structures. During this process, the weight functions in hidden layers are optimized so they can relate input to output correctly. When the sufficiently trained network processes an unknown sequence, it applies the rules learned in training to recognize particular structural patterns.

11. Which of the following is untrue regarding Prediction with Neural Networks?
a) When multiple sequence alignments and neural networks are combined, the result is further improved accuracy
b) A neural network is trained by a single sequence
c) A neural network is trained by a sequence profile derived from the multiple sequence alignment
d) When the sufficiently trained network processes an unknown sequence, it applies the rules learned in training to recognize particular structural patterns

View Answer

Answer: b [Reason:] A neural network is trained not by a single sequence but by a sequence profile derived from the multiple sequence alignment. This combined approach has been shown to improve the accuracy to above 75%, which is a breakthrough in secondary structure prediction. The improvement mainly comes from enhanced secondary structure signals through consensus drawing. The following lists several frequently used third generation prediction algorithms available as web servers.

12. Which of the following is untrue regarding PHD?
a) It stands for Profile network from Heidelberg
b) It is a web-based program that combines neural network only
c) It first performs a BLASTP of the query sequence against a non redundant protein sequence database
d) In initial steps it finds a set of homologous sequences, which are aligned with the MAXHOM program (a weighted dynamic programming algorithm performing global alignment)

View Answer

Answer: b [Reason:] is a web-based program that combines neural network with multiple sequence alignment. After the initial steps, the resulting alignment in the form of a profile is fed into a neural network that contains three hidden layers. The first hidden layer makes raw prediction based on the multiple sequence alignment by sliding a window of thirteen positions.