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The correct ANSWER is (c) Abagyan and Batalov, in 1997

For explanation I would say: Abagyan and Batalov, in 1997, suggested the above observation. HOWEVER, since the scoring system that they used favored LOCAL alignments, these alignments they produced may not be global but local. Unfortunately, there is no EQUIVALENT theory on which to base an analysis of global alignment scores as there is for local alignment scores.

Correct choice is (a) the more significant is the alignment

The best explanation: In the scoring system, the higher this score, the more significant is the alignment, or the more it resembles alignments in related proteins. ALSO, the score GIVEN for gaps in aligned SEQUENCES is NEGATIVE, because such misaligned regions should be uncommon in sequences of related proteins. Such a score will reduce the score obtained from an adjacent, matching region upstream in the sequences.

The correct answer is (b) False

The explanation is: Those isolated DOTS represent RANDOM matches. The dots on the diagonal represent the perfect alignment and the dots with vertical and horizontal shifts show INSERTIONS and deletions.

Correct choice is (c) Alignments are further checked but not refined by HUMAN annotators before HMM profile construction

To elaborate: Alignments are further checked and refined by human annotators before HMM profile construction. Protein functions are also manually curated. Thus, the database may be of better quality than PFAM with more extensive functional annotations. Compared to Pfam,

The SMART database contains an independent collection of HMMs, with emphasis on signaling, extracellular, and chromatin-associated MOTIFS and domains. Sequence searching in this database produces a graphical output of domains with well-annotated information with respect to cellular LOCALIZATION, functional sites, super-family, and tertiary structure.

Right ANSWER is (c) This does not HELP in DETERMINING evolutionary relationship

For explanation I would say: Needleman-Wunsch algorithm is used when 2 genes that are ALREADY understood as CLOSELY related and can be used to understand them in further details. This is quite helpful in finding orthologs, paralogs and homologs in evolutionary studies.

The correct answer is (a) Lipman, in 1984

The explanation: When the RANDOMIZED sequences were prepared by shuffling the SEQUENCE to conserve base composition, as was done by Dayhoff and others, the standard deviation was approximately one-third less than the distribution of scores of the natural sequences. Thus, natural sequences are more variable than randomized ONES, and using such randomized sequences for a significance TEST may lead to an overestimation of the significance.

Right option is (d) It STANDS for Percent Altered Mutation

Easy explanation: PAM stands for Percent Accepted Mutation. In this, each matrix gives the changes expected for a given PERIOD of evolutionary time, evidenced by decreased sequence similarity as genes encoding the same protein DIVERGE with increased evolutionary time.

Right answer is (a) True

Easy explanation: The odds scores are converted to log odds scores so that the values for amino acid pairs in an alignment may be summed to obtain the log odds score of the alignment. In this case, the logarithms are calculated to the BASE 2 and multiplied by 2 to GIVE values DESIGNATED as half-bits (a BIT is the UNIT of an odds score that has been converted to a logarithm to the base 2). The value of 4 indicates that the 4 amino acid alignment is 2(4/2) = 4 four-fold more likely than expected by chance.

The correct answer is (d) They are USEFUL in small SCALE databases

Explanation: k-tuple or word methods are especially useful in large-scale DATABASE searches where a large proportion of stored sequences will have essentially no significant match with the query sequence. They are HEURISTIC methods that are not guaranteed to find an optimal ALIGNMENT solution but are significantly more efficient than Smith-Waterman algorithm.

The correct CHOICE is (d) FIRST ROW and first COLUMN are set to zero

For explanation I would say: INITIALIZATION and scoring system of the Smith–Waterman algorithm and Needleman-Wunsch algorithm is quite different. In global alignment first row and first column are subject to gap penalty and are not set to 0.

Correct option is (b) two, HIGHEST scoring

The explanation: These blocks are then joined in VARIOUS combinations to produce alignments.

There is no need for GAP penalties because only the aligned sequence positions in blocks are scored. Instead of using a given substitution matrix and gap scoring system to FIND the highest scoring ALIGNMENT, a Bayesian statistical approach is used.

The CORRECT choice is (b) very HIGH scores

Easiest explanation: The significance of the scores of global alignments, is more DIFFICULT to determine. Using the Needleman-Wunsch ALGORITHM and a suitable scoring system, there are many ways to produce a global alignment between any pair of sequences, and the scores of many different alignments may be quite similar hence the scores obtained might be unusually high.

The correct CHOICE is (a) INCREASES the matching of identical amino acids at subsequent portions in the ALIGNMENT

Explanation: In the alignment process, gaps are added to the alignment in a manner that increases the matching of identical or similar amino acids at subsequent portions in the alignment. Ideally, when two similar protein sequences are ALIGNED, the alignment should have long regions of identical or related amino ACID pairs and very few gaps. As the sequences become more distant, more mismatched amino acid pairs and gaps should appear.

Correct CHOICE is (B) Doesn’t allow you to specify threshold

The explanation: The EMBOSS DOTTUP doesn’t allow you to specify threshold but allows you to specify WINDOW size. Also, if all cells in the window are identity, it colors in all the cells in the window.

Correct answer is (c) Gibbs and McIntyre

The best explanation: The first computer aided SEQUENCE comparison is called “dot-matrix ANALYSIS” or simply dot-plot. The first published ACCOUNT of this method is by Gibbs and McIntyre (1970 The diagram, a method for comparing SEQUENCES. Eur. J. BIOCHEM 16: 1-11).

The correct option is (d) These MATRICES are LOGARITHMIC identity values

The best I can explain: These matrices are actual percentage identity values. Or SIMPLY, they depend on similarity. BLOSUM 62 means there is 62 % similarity.

The CORRECT answer is (c) an alignment algorithm and a particular scoring matrix

Explanation: ANALYSIS of the yeast and C. elegans genomes for such repeats has underscored the importance of using a range of DNA scoring MATRICES such as PAM1 to

PAM120 if most repeats are to be found. The application of the above Bayesian analysis allows a DETERMINATION of the probability distributions as a function of both LENGTH of the repeated region and evolutionary distance.

Right choice is (a) True

For explanation: If both mismatches and gaps are HEAVILY penalized, the resulting ALIGNMENT will also be a local alignment that CONTAINS the longest region of exact matches. In the above two cases, the alignment score of the highest-scoring local alignment will increase as the logarithm of the length of the sequences. Under these same conditions, the score of the CORRESPONDING global alignment between the sequences will be negative.

Right choice is (d) This METHOD doesn’t provide an optimal (highest scoring) alignment

For explanation: The method of SEQUENCE alignment by dynamic programming provides an optimal (highest scoring) alignment as an output. The quality of the alignment between two sequences is calculated using a scoring system that favors the matching of related or IDENTICAL amino ACIDS and penalizes for poorly matched amino acids and GAPS.

The correct answer is (a) True

The best EXPLANATION: Once those parameters have been SET, the resulting ALIGNMENT for two sequences should always be the same. Hence, the use of the dynamic PROGRAMMING method requires a scoring system for the comparison of symbol pairs (nucleotides for DNA sequences and amino acids for protein sequences), and a scheme for insertion/deletion (GAP) penalties.

Right answer is (d) Change or MUTATE residues

Easiest explanation: The gap penalties mentioned above are for the determination of score of the ALIGNING sequences. The change in residue barely takes place as there are number of other softwares for that PURPOSE and also the main OBJECTIVE is to FIND the score of the alignment.

Correct answer is (a) FASTA is faster than BLAST

The best I can explain: BLAST is faster than FASTA and most other tools. The speed and RELATIVELY good ACCURACY of BLAST is the KEY why the tool is the most popular bioinformatics search tool.

The correct CHOICE is (b) False

Explanation: The REPEATING elements would be represented in parallel lines in repetitive manner. BETTER is the repetition; better is the nature of parallel lines. Also, the INTERSECTIONS show the pallindromic sequences.

Right choice is (b) Agarwal and States, 1996

The best I can explain: Agarwal and States, in1996, have applied BAYESIAN methods to provide the best estimate of the evolutionary distance between TWO DNA sequences. For example, sequences of the same LENGTH that have a certain LEVEL of mismatches.

Correct choice is (b) Gumbel extreme value DISTRIBUTION

The best explanation: Originally, the significance of sequence alignment scores was evaluated on the basis of the assumption that alignment scores followed a normal STATISTICAL distribution. If sequences are randomly generated in a computer by a Monte Carlo or sequence SHUFFLING method, as in generating a sequence by picking marbles representing four bases or 20 amino acids out of a bag, the distribution may look normal at first glance. But on further ANALYSIS the above RESULT was obtained.

Correct CHOICE is (B) WebLogo

To elaborate: In WebLogo, a user needs to enter the SEQUENCE alignment in FASTA format to allow the program to compute the logos. A graphic file is returned to the user as a RESULT.

The CORRECT option is (a) height, RELATIVE frequency

For explanation: The height expresses the data about the extent of the conservation of the position and each LETTER SHOWS the frequency of that particular residue. The amplitude, here in this case, is irrelevant option.

Correct CHOICE is (a) Protein relatedness is DEFINED by the P-values from the BLAST alignments

The best I can explain: InterPro is a DATABASE of clusters of homologous PROTEINS similar to COG. Protein relatedness is defined by the E-values from the BLAST alignments. The database further provides gene ontology information for protein cluster at each level as well as keywords from InterPro domains for functional prediction.

The correct choice is (d) A specific MUTATIONAL MODEL is required

To elaborate: One disadvantage of the BAYESIAN approach is that a specific mutational model is required, whereas other methods, such as the maximum likelihood approach, can be used to estimate the BEST mutational model as well as the distance. Computationally, however, the Bayesian method is much more practical.

Correct ANSWER is (d) gap penalties

Best EXPLANATION: These program suites include default gap penalties. When deciding gap penalties for local alignment programs, a CONSIDERATION is that the penalties should be large enough to provide a local alignment of the SEQUENCES.

Right answer is (c) wx = g + RX

For explanation I WOULD SAY: wx = g + rx is the equation where x is the LENGTH of the gap. in some formulations of the gap penalty, the equation wx= g+ r (x – 1) is used. Thus, the gap extension penalty is not added to the gap opening penalty until the gap size is 2.

Correct choice is (a) True

The EXPLANATION is: There is a very large NUMBER amino acid scoring MATRICES in use, some much more popular than others, and these scoring matrices are designed for different purposes. Some, such as the Dayhoff PAM matrices, are based on an evolutionary model of protein change, whereas others, such as the BLOSUM matrices, are designed to IDENTIFY members of the same family. Alignments between DNA sequences require similar kinds of considerations.

The correct CHOICE is (d) BLOSUM-X type uses logarithmic identity to find similarity

The best explanation: BLOSUM-X type identifies SEQUENCES that are X% similar to the query sequence i. E. score 54 corresponds to 54% similarity hence reducing the complexity of the output and giving the similarity in percentage. ALSO, these matrices are popular in bioinformatics DUE to their speed and accuracy.

Right choice is (d) Literature mining

The explanation: All the REST of the options are indeed valid and proven mathematical methods that contain efficient algorithms in finding motifs in PROTEIN sequences. Literature mining is not a mathematical algorithm or tool as such to be used in identifying motifs. But it is definitely a part of research when it COMES to find a FUNCTION of various protein sequences.

Correct option is (C) 1981

Explanation: The algorithm was first PROPOSED by Temple F. Smith and Michael S. Waterman in 1981. The Smith–Waterman algorithm performs local sequence ALIGNMENT; that is, for determining similar regions between two STRINGS of nucleic ACID sequences or protein sequences.

Correct ANSWER is (c) It is useful when the ALIGNING sequences are dissimilar

The best I can EXPLAIN: Performing global alignment is most useful when the aligning sequences are SIMILAR and of roughly the same size. This is most useful to find the similarities among the ORGANISMS that are roughly connected on the timeline.

Right choice is (d) The functional annotation of blocks is not consistent with that for the MOTIFS

To elaborate: BLOCKS is a database that uses multiple alignments derived from the most conserved, ungapped regions of homologous protein sequences. Because blocks often ENCOMPASS motifs, the functional annotation of blocks is thus consistent with that for the motifs. A query sequence can be USED to align with pre-computed profiles in the database to select the highest scored MATCHES. Because of the use of the weighting SCHEME, the signal-to-noise ratio is improved relative to PRINTS.

The correct option is (d) It is a PROTEIN family database based on structural CLASSIFICATION

The explanation is: COG which STANDS for Cluster of Orthologous Groups, is a protein family database based on phylogenetic classification. Because orthologous proteins shared by three or more lineages are considered to have descended through a VERTICAL evolutionary scenario, if the FUNCTION of one of the members is known, functionality of other members can be assigned.

Correct option is (a) SCOP

To ELABORATE: The SIGNATURES from INTERPRO come from 11 member databases viz. CATH-Gene3D, HAMAP, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY, TIGRFAMs.

Correct choice is (a) it is assumed that each amino acid position is equally mutable

Explanation: In this process, first, it is assumed that each amino acid position is equally mutable, whereas, in fact, SITES VARY CONSIDERABLY in their DEGREE of mutability. Mutagenesis HOT spots are well known in molecular genetics, and variations in mutability of different amino acid sites in proteins are well known.

Correct option is (d) Japan

Explanation: Pfam is available at FOUR locations around the world each PROVIDING a core SET of functionality for ACCESSING each family. They are US, UK, Sweden and France. Documentation on the CONTENT and use of Pfam is available via the web.

Right choice is (a) positive and negative values

For explanation I would say: These MATRICES contain positive and negative values, reflecting the likelihood of each AMINO acid substitution in related proteins. Using these tables, an alignment of a sequential set of amino acid pairs with no gaps RECEIVES an overall score that is the sum of the positive and negative log odds scores for each INDIVIDUAL amino acid pair in the alignment.

The CORRECT choice is (b) False

The explanation: After the derivation, the outputs of the dynamic programming are the RATIOS are called odd scores. The ratios are transformed to logarithms of odds scores, called LOG odds scores, so that scores of sequential pairs may be added to reflect the overall odds of a REAL to chance alignment of an alignment. This happens in DAYHOFF PAM250 and BLOSUM62.

Correct answer is (c) 1970

The best I can explain: This method was FIRST described in 1970. Briefly, this method involves constructing a matrix with one of the SEQUENCES to be compared running HORIZONTALLY across the BOTTOM, and the other running vertically along the left-hand SIDE.

Right option is (a) fewer

The EXPLANATION: The options MAXIMUM and minimum are comparatively OBSOLETE as there involves the studies of alignment. Conserved positions have fewer residues and bigger symbols; whereas less conserved positions have a more heterogeneous mixture of smaller symbols stacked together. In GENERAL, a SEQUENCE logo provides a clearer description of a consensus sequence.

The CORRECT option is (a) MULTIPLE Expectation Maximization for Motif ELICITATION

Easy explanation: Multiple Expectation Maximization for Motif Elicitation is a web-based PROGRAM that uses the EM algorithm to find motifs either for DNA or protein sequences. It uses amodified EM algorithm to avoid the local MINIMUM problem.