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Right option is (c) It FIRST aligns two sequences using the Needleman-Wunsch algorithm and calculates the score

To EXPLAIN: It first aligns two sequences using the Smith–Waterman algorithm and calculates the score. The shuffled sequence is realigned with the unshuffled sequence. The resulting alignment score is recorded. This PROCESS is iterated many (normally 1,000) times to help generate data for fitting the Gumble DISTRIBUTION.

The correct CHOICE is (a) The pool of alignment scores from the shuffled sequences

To explain I would say: Maximum scores are OBTAINED through repeated shuffling. Then the pool of alignment scores from the shuffled sequences is USED to generate parameters for the EXTREME distribution. The original alignment score is then compared against the distribution of random alignments to determine WHETHER the score is beyond random chance.

Correct option is (a) True

To explain: After the MENTIONED STEP, COMPUTATION for the alignment score for the shuffled sequence pair is done. Further, More such SCORES are SIMILARLY obtained through repeated shuffling.

Right answer is (a) True

For explanation I WOULD say: The statistics in the test were derived from ungapped LOCAL sequence alignments. Hence, it is not known whether the Gumble distribution applies equally well to gapped alignments. However, for all practical purposes, it is reasonable to assume that scores for gapped alignments essentially fit the same distribution. A FREQUENTLY used SOFTWARE program for assessing statistical significance of a PAIRWISE alignment is the PRSS program.

Correct option is (a) unlikely, significant

Best explanation: The extreme margin of the distribution DENOTES the likeliness and thus significance. A P-value is given to indicate the PROBABILITY that the original ALIGNMENT is DUE to random chance.

The correct answer is (b) False

Best EXPLANATION: The MAJOR feature of the program is that it allows partial shuffling. For example, shuffling can be restricted to residues within a local WINDOW of 25–40, whereas the residues outside the window REMAIN UNCHANGED.

Correct option is (b) UNRELATED sequences of the same LENGTH are then generated through a RANDOMIZATION PROCESS

To explain I would say: Unrelated sequences of the same length are then generated through a randomization process in which one of the two sequences is randomly shuffled. And the NEXT step is that a new alignment score is computed for the shuffled sequence pair.

Right answer is (d) Gumble extreme value distribution

To explain I WOULD say: The mentioned Distribution PATTERN matches the Gumble extreme value distribution for which a mathematical expression is AVAILABLE. This means that, given a sequence SIMILARITY value, by using the mathematical formula for the extreme distribution, the statistical SIGNIFICANCE can be accurately estimated.

Right option is (b) UNRELATED, randomized

For EXPLANATION: Solving the statistical significance PROBLEM requires a statistical test of the alignment scores of two unrelated sequences of the same length. From the DISTRIBUTION, a statistical test can be performed BASED on the number of standard deviations from the average score.

Correct answer is (a) True

The explanation: In the self comparison, there is a main DIAGONAL for perfect MATCHING of each RESIDUE. If REPEATS are present, short parallel lines are OBSERVED above and below the main diagonal.

The correct ANSWER is (a) True

Easy explanation: Dots are only placed when a stretch of RESIDUES equal to the window SIZE from one sequence matches completely with a stretch of another sequence. This method has been shown to be EFFECTIVE in reducing the noise level. The window is also called a tuple, the size of which can be manipulated so that a clear PATTERN of sequence match can be plotted. However, if the selected window size is too long, sensitivity of the alignment is lost.

The CORRECT option is (a) True

For explanation: For determining a homology RELATIONSHIP of two protein sequences, for example, if both sequences are aligned at full length, which is 100 residues long, an identity of 30% or higher can be SAFELY regarded as having close homology. If their identity level falls between 20% and 30%, determination of homologous relationships in this range becomes less certain.

The correct option is (c) It is not useful in identifying chromosomal repeats

The BEST EXPLANATION: It is useful in identifying chromosomal repeats and in comparing gene order conservation between two closely related genomes. The dot matrix method gives a direct visual statement of the relationship between two sequences and helps easy IDENTIFICATION of the regions of GREATEST similarities. The method thus has some APPLICATIONS in genomics.

The correct answer is (a) True

Easiest explanation: There are EXAMPLES of such paralogous genes that have distinct functions but SIMILAR origin. In that case, the DISTANT evolutionary relationships have to be detected USING other methods.

Right answer is (a) unlikely

To explain I would say: Sequence ALIGNMENT provides inference for the relatedness of two sequences under study. Regions that are aligned but not IDENTICAL represent residue substitutions; regions which RESIDUES from ONE sequence correspond to nothing in the other represent INSERTIONS or deletions that have taken place on one of the sequences during evolution.

The correct answer is (d) It is the PROCESS of aligning multiple sequences

Explanation: Pair wise sequence alignment is the process of aligning two sequences and is the basis of database SIMILARITY searching and multiple sequence alignment. As NEW BIOLOGICAL sequences are being GENERATED at exponential rates, sequence comparison is becoming increasingly important to draw functional and evolutionary inference of a new protein with proteins already existing in the database.

The correct choice is (d) The molecular sequences barely UNDERGO CHANGES

Easiest explanation: During this TIME period, the molecular sequences undergo random changes, some of which are selected during the process of evolution. As the selected sequences gradually accumulate mutations and DIVERGE over time, traces of evolution may still remain in certain portions of the sequences to allow identification of the COMMON ancestry.

The correct answer is (b) False

The best explanation: The degree of sequence conservation in the alignment reveals evolutionary relatedness of different SEQUENCES, WHEREAS the variation between sequences reflects the changes that have OCCURRED during EVOLUTION in the form of substitutions, insertions, and deletions. Identifying the evolutionary relationships between sequences helps to characterize the function of UNKNOWN sequences. When a sequence alignment reveals significant similarity among a group of sequences, they can be considered as belonging to the same family.

The correct answer is (B) PERCENTAGES, qualitative

To elaborate: SIMILARITY is a direct RESULT of observation from the sequence Alignment. For example, one MAY say that two sequences share 40% similarity. It is incorrect to say that the two sequences share 40% homology. They are either homologous or nonhomologous.

Right choice is (c) diagonal

For explanation: The dots LINE up to FORM contiguous diagonal lines, which REVEAL the sequence alignment. If there are interruptions in the middle of a diagonal line, they indicate insertions or deletions. Parallel diagonal lines within the matrix represent REPETITIVE regions of the sequences.

The correct OPTION is (a) horizontal and vertical axes

To elaborate: The comparison is done by scanning each residue of ONE SEQUENCE for similarity with all residues in the other sequence. If a residue match is FOUND, a dot is placed within the graph. Otherwise, the matrix positions are left BLANK.

Correct option is (b) False

The best explanation: The two sequences to be aligned can be of DIFFERENT LENGTHS. This approach is more appropriate for ALIGNING divergent biological sequences CONTAINING only modules that are similar, which are referred to as domains or motifs. This approach can be used for aligning more divergent sequences with the goal of searching for conserved patterns in DNA or protein sequences.

The correct choice is (a) True

Easy explanation: The goal of pair wise sequence ALIGNMENT is to find the best pairing and to achieve this goal; one sequence needs to be shifted RELATIVE to the other to find the position where maximum matches are found. There are two DIFFERENT alignment strategies that are often used: global alignment and LOCAL alignment.

Right choice is (a) True

Explanation: The RESIDUES that perform key functional and structural ROLES tend to be preserved by NATURAL selection. For example, active site residues of an enzyme family tend to be conserved because they are RESPONSIBLE for catalytic functions. Therefore, by comparing sequences through alignment, PATTERNS of conservation and variation can be identified.

Right choice is (a) Two sequences can homologous relationship even if have do not have common origin

For EXPLANATION I WOULD say: Homologous RELATIONSHIPS are more certain when the sequences have common evolutionary origin. A RELATED but different term is sequence similarity, which is the percentage of aligned residues that are similar in physiochemical properties such as SIZE, charge, and hydrophobicity.

Correct option is (b) False

Easy explanation: Self COMPLEMENTARITY of DNA sequences, also CALLED inverted repeats can be identified using a DOT plot. For example, those that forms the STEMS of a hairpin STRUCTURE. In this case, a DNA sequence is compared with its reverse-complemented sequence. Parallel diagonals represent the inverted repeats.

Right option is (a) True

The explanation: Both types of ALGORITHMS can be based on one of the three methods: the dot matrix method, the DYNAMIC programming method, and the word method. The word method is used in FAST DATABASE similarity searching.