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Correct answer is (b) False

The best I can explain: Match-Box compares segments of every nine residues of all possible pair wise alignments. It is a web-based server that also aims to identify conserved blocks (or BOXES) among sequences. The PROGRAM compares segments of every nine residues of all possible pair wise alignments. If the similarity of particular segments is above a certain threshold across all sequences, they are USED as an anchor to ASSEMBLE MULTIPLE alignments; residues between blocks are unaligned.

Correct ANSWER is (B) False

The best explanation: MACAW is both a local multiple sequence alignment program and a sequence editing tool. Given a set of SEQUENCES, the program finds ungapped blocks in the sequences and gives their statistical significance. Later versions of the program find blocks by one of three user-chosen METHODS.

The CORRECT option is (a) available, sufficiently LARGE, not too complex

To elaborate: The more abundant AMINO acids already found in that column would probably be favored. Thus, if a good sampling of sequences is available, the number of sequences is sufficiently large, and the MOTIF structure is not too complex, it should, in principle, be possible to obtain frequencies HIGHLY representative of the same motif in other sequences also (Henikoff and Henikoff 1996).

The correct answer is (b) It is dissimilar to the principle of the EM METHOD

Explanation: It is ANOTHER STATISTICAL method for finding motifs in SEQUENCES is the Gibbs sampler. The method is similar in principle to the EM method described above, but the algorithm is different. A combinatorial approach of the Gibbs sampler and MOTIF may be used to make blocks at the BLOCKS Web SITE.

The correct choice is (a) True

Explanation: As more sequences are added to a PROFILE of an existing MSA, gaps accumulate and influence the ALIGNMENT of further sequences. CLUSTALW CALCULATES gaps in a NOVEL way designed to place them between conserved domains.

Right answer is (a) True

The explanation is: The exhaustive alignment method involves examining all possible aligned positions simultaneously. SIMILAR to dynamic programming in pair wise alignment, which involves the use of a two-dimensional MATRIX to SEARCH for an optimal alignment, to use dynamic programming for multiple sequence alignment, EXTRA dimensions are needed to TAKE all possible ways of sequence matching into consideration.

Correct answer is (a) True

Best EXPLANATION: This is because these formats follow a precise OUTLINE, one may be readily converted to another by computer programs. READSEQ by D.G.Gilbert at INDIANA University at Bloomington is one such PROGRAM.

Right choice is (a) True

The explanation is: The PROGRAM MSASA (MULTIPLE Sequence Alignment by SIMULATED Annealing) starts with a heuristic MSA (Multiple Sequence Alignment). Further, it CHANGES the alignment by following an algorithm designed to identify changes that increase the alignment score.

The correct option is (b) The initial heuristic ALIGNMENT obtained by MSA is calculated in a different way

Explanation: The initial heuristic alignment obtained by MSA is calculated the same way, although it performs a global-multiple sequence alignment by a different method than MSA (Multiple Sequence Alignment). As the MENTIONED options are first two steps, the last is aligning the SEQUENCES SEQUENTIALLY, guided by the PHYLOGENETIC relationships indicated by the tree.

Right choice is (b) \(\frac{2^{2N}}{\sqrt{πN}}\)

For EXPLANATION I would SAY: 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 10^149.

The correct option is (d) Pattern blocking

For explanation I would SAY: Pattern Searching is the correct name of the method for finding localized sequence similarity. This type of analysis was performed on groups of RELATED PROTEINS, and the amino acid patterns that were located may be FOUND in the PROSITE catalog.

The correct option is (b) False

The best explanation: The HMM is a statistical model that CONSIDERS all possible COMBINATIONS of matches, mismatches, and gaps to generate an alignment of a set of sequences. A localized region of similarity, including insertions and deletions, may also be modeled by an HMM. Analysis of sequences by an HMM is discussed on page 185 ALONG with other statistical methods.

Correct choice is (a) True

The explanation: The SEQUENCES to be aligned are WRITTEN in rows, as on a page, except that they are made to OVERLAP by a random amount of sequence, up to 50 residues long for sequences about 200 in length. The ends are then padded with gaps. A TYPICAL population of 100 of these MSAs is made, although other numbers may be set.

Right choice is (B) False

The best EXPLANATION: 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.

Right option is (a) True

Best EXPLANATION: It is truly an ADVANTAGE of MULTIPLE sequence alignment. For example, it allows the identification of conserved sequence patterns and motifs in the whole sequence family, which are not obvious to DETECT by comparing only two sequences.

Correct choice is (d) The row-by-column composition of the site already available is used to estimate the probability

Easiest explanation: The EM algorithm then consists of two steps, which are repeated consecutively. In step 1, the EXPECTATION step, the column-by-column composition of the site already available is used to estimate the probability of finding the site at any position in each of the sequences. These PROBABILITIES are used in turn to PROVIDE new information as to the expected base or amino acid DISTRIBUTION for each column in the site.

Correct OPTION is (a) True

To explain: This is indeed the drawback of that method. For this reason, full dynamic programming is limited to small DATASETS of less than ten SHORT sequences. For the same reason, few multiple alignment programs employing this “brute force” approach are PUBLICLY available.

Right option is (a) True

For explanation I WOULD say: Two examples of programs that use progressive METHODS are CLUSTALW and the Genetics COMPUTER Group program PILEUP. CLUSTALX provides a graphic interface.

These changes provide more realistic alignments that should reflect the evolutionary changes in the aligned sequences and the more APPROPRIATE distribution of gaps between conserved domains.

Right option is (a) True

The explanation: The BASE composition of each COLUMN in the aligned patterns is then determined. The composition of the flanking sequence on each side of the site provides the surrounding base or amino acid composition for COMPARISON. Each sequence is assumed to be the same length and to be aligned by the ENDS.

Right answer is (a) True

The best EXPLANATION: These ungapped patterns may be EXTRACTED from these aligned regions and used to produce blocks. Blocks FOUND in this manner are only as good as the MSA from which they are DERIVED. A global MSA of related PROTEIN sequences usually includes regions that have been aligned without gaps in any of the sequences.

Correct answer is (b) False

For explanation: 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.

Correct OPTION is (d) This method is not based on heuristic methods

For explanation: This method is based on heuristic methods. The procedure starts by producing a low-quality ALIGNMENT and GRADUALLY improves it by iterative REALIGNMENT through well-defined procedures until no more IMPROVEMENTS in the alignment scores can be achieved.

Correct choice is (c) In this method the use of affine gap penalties, long GAPS is ALLOWED, and, in some cases, this may limit the accuracy of the method

To explain I would say: Another major limitation is the “greedy” nature of the algorithm: it depends on initial pair WISE alignment. Once gaps introduced in the early STEPS of alignment, they are fixed. The final alignment could be far from optimal. The problem can be more glaring when dealing with divergent sequences.

Right option is (a) True

Best explanation: For such divergent sequences that share only regional SIMILARITIES, a local alignment based approach has to be used. The strategy IDENTIFIES a BLOCK of ungapped alignment SHARED by all the sequences, hence, the block-based local alignment strategy.

The correct CHOICE is (a) True

The best I can explain: A natural extension of pair WISE alignment is multiple SEQUENCE alignment, which is to ALIGN multiple related sequences to achieve optimal matching of the sequences. Related sequences are identified through the database similarity searching. As the process generates multiple matching sequence pairs, it is often necessary to convert the numerous pair wise alignments into a single alignment, which arranges sequences in such a way that EVOLUTIONARILY equivalent positions across all sequences are matched.

Right answer is (d) This method does not contribute much to degenerate polymerase CHAIN reaction (PCR) primers creation

The explanation: In practice, heuristic approaches are most often used. MULTIPLE sequence ALIGNMENT has applications in designing degenerate (PCR) primers based on multiple related SEQUENCES.