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Right option is (d) added

To explain: An EXAMPLE is the calculation of the ODDS score for a given sequence alignment using a series of alternative PAM SCORING matrices. The alignment scores are calculated in log odds units and then CONVERTED into odds scores.

The CORRECT OPTION is (a) True

To EXPLAIN I would say: There are MANY factors that influence both the location and TYPES of amino acid changes that occur in proteins. Wilbur (1985) has tested the Markov model of evolution and has shown that it can be valid if certain changes are made in the way that the PAM matrices are calculated.

Right option is (c) CDART is a substitute for individual DATABASE searches

The BEST I can EXPLAIN: CDART is a domain search program that combines the results from various database searches. As with InterPro, CDART is not a substitute for individual database searches because it often MISSES certain features that can be FOUND in SMART and Pfam.

The correct CHOICE is (b) local alignments, GLOBAL alignments

Best explanation: Smith-Waterman alignment algorithm and the SCORING system USED to produce a local alignment are designed to reveal regions of closely matching sequence with a positive alignment score. In random or unrelated sequence alignments, these regions are rarely found. Hence, their presence in real sequence alignments is significant, and the PROBABILITY of their occurring by chance alignment of unrelated sequences can be readily calculated.

Right answer is (a) True

Explanation: For an ALGORITHM, the output depends on the choice of a scoring system. For protein sequences, the simplest system of COMPARISON is one based on identity. A match in an alignment is only SCORED if the two aligned amino acids are identical. However, one can also examine related protein sequences that can be aligned EASILY and find which amino acids are commonly SUBSTITUTED for each other.

The correct OPTION is (a) SIMMI

Easiest EXPLANATION: For the purpose of DOT plot interpretation there are various softwares currently present. Among these SIM is used for these KINDS of alignments through dot-plot method that is WRONGLY abbreviated.

Right answer is (d) Even if no WORDS are similar, there is an alignment to be considered

To explain I would SAY: If no words are similar, there is no alignment i. e. it will not find MATCHES for very short SEQUENCES. But it is considerably accurate as compared to other tools and hence is QUITE popular.

The correct answer is (d) For TWO sequences of LENGTH m and n, the matrix to be defined should be of dimensions m and n

The explanation: For two sequences of length m and n, the matrix to be defined should be of dimensions m+1 and n+1so that there is margin for ADDITION of the score along the diagonal. ALSO, corresponding score is further calculated at the end cumulatively.

Right OPTION is (c) Hidden Markov models (HMMs) are not used in PANTHER

Easy explanation: In PANTHER the subfamilies model the DIVERGENCE of specific functions within protein families, allowing more accurate association with FUNCTION (human-curated molecular function and biological process classifications and pathway diagrams), as well as inference of amino acids important for functional specificity. Hidden Markov models (HMMs) are built for each family and subfamily for classifying additional protein sequences.

The correct option is (B) Protein Data BANK

Best EXPLANATION: The source of protein STRUCTURES in SCOP is PDB (Protein Data Bank). PDB is a secondary database which MEANS it has protein structures derived from primary databases that have the protein sequences. UNIPROT is a primary database.

The CORRECT choice is (a) True

For explanation I would say: In genomes, the presence of repeats may be revealed by LONG regions of matched SEQUENCE POSITIONS dispersed among regions of sequence positions that do not match. However, as the frequency of mismatches is increased, it becomes difficult to determine the extent of the repeated region.

Right CHOICE is (B) multiplied

To ELABORATE: An example is the calculation of the odds of an alignment of two sequences from the alignment scores for each of the matched pairs of bases or amino acids in the alignment. The odds scores for the pairs are multiplied. Usually, the LOG odds score for the first pair is added to that for the second, etc., until the scores for EVERY pair have been added.

Right choice is (a) SHORT, partially conserved

To explain I would SAY: Gibbs sampling approach to look for short, partially conserved gap-free segments for either DNA or protein SEQUENCES. To ensure ACCURACY, more than twenty sequences of the exact same LENGTH should be used.

The correct option is (c) DISTINCTLY related SEQUENCES that share common MOTIFS

For explanation I would say: Often, distantly related sequences that share common motifs cannot be readily aligned. For example, the sequences for the helix-turn-helix motif in transcription factors can be subtly different ENOUGH that traditional multiple sequence alignment approaches fail to generate a satisfactory answer. For detecting such subtle motifs, more sophisticated algorithms such as expectation maximization (EM) and Gibbs sampling are USED.

Correct CHOICE is (a) Score can be negative

For explanation I would say: Score can be negative. When any element has a score lower than zero, it means that the sequences up to this position have no SIMILARITIES; this element will then be set to zero to eliminate influence from PREVIOUS ALIGNMENT. In this way, calculation can continue to find alignment in any position AFTERWARD.

Correct choice is (c) AlignACE

The BEST explanation: The GIBBS sampling algorithm can identify multiple motifs in a sequence in a sequence set using iterative masking procedure. It is used in AlignACE whereas BEST is a suite of four motif discovery tools integrated in a graphical user interface. Also, CONSENSUS program finds motifs in a set of UNALIGNED sequences and PhyloCon builds on this framework by modeling conservation across ORTHOLOGOUS genes from multiple species.

The correct answer is (c) SCOP was created in 1994 in the CENTRE of Protein Engineering and the University College London

The best explanation: SCOP, Structural Classification of Proteins, was created in 1994 in the Centre of Protein Engineering and the LABORATORY of Molecular Biology. It was maintained by Alexey G. Murzin and his COLLEAGUES in the Centre for Protein Engineering until its closure in 2010 and subsequently at the Laboratory of Molecular Biology in Cambridge, ENGLAND.

The correct choice is (a) True

To elaborate: The BLOSUM matrices are based on scoring SUBSTITUTIONS found over a RANGE of evolutionary periods and reveal that substitutions are not always as predicted by the PAM MODEL. The PURPOSE of assumption in this evolutionary model is to make predictions.

Right choice is (c) Local ALIGNMENTS have terminal gaps

To EXPLAIN: Local alignments never have terminal gaps, because a higher SCORE could be OBTAINED by deleting the gaps (which always have negative scores, i.e. penalties). In case of global alignment there are terminal gaps while analyzing.

Correct option is (B) It stands for Point Altered Mutations

To EXPLAIN I would say: PAM stands for Point Accepted Mutations. PAM matrices are calculated by OBSERVING the differences in closely related proteins. One PAM unit (PAM1) specifies one accepted point mutation per 100 amino acid residues, i.e. 1% change and 99% remains as such.

Correct answer is (a) True

The explanation is: The assumption mentioned above (the molecular CLOCK hypothesis) is MADE to REDUCE the complications. Such problems may be SOLVED by scoring different portions of a sequence with a different scoring matrix, and then using the above Bayesian methods to calculate the best EVOLUTIONARY distance.

Correct option is (d) The log ODDS scores of the PSSM are modified at the end of the process

The explanation is: The log odds scores of the PSSM are modified in each iteration to maximize the alignment of the matrix to each sequence. During the ITERATIONS, the sequence pattern for the conserved motifs is GRADUALLY “RECRUITED” to the PSSM.

Right answer is (d) For finding HUGE regions within SEQUENCES

Explanation: As used in a computer program called RELATE (Dayhoff 1978), all possible segments of a given length of one sequence are compared with all segments of the same length from another. An alignment score using a scoring matrix is obtained for each comparison to GIVE a score distribution among all of the segments. A segment comparison score in STANDARD deviation units is calculated as the difference between the values for real sequences minus the average value for random sequences DIVIDED by the standard deviation of the scores from the random sequences.

Right ANSWER is (b) False

The best explanation: The Dayhoff Model of PROTEIN Evolution as Used in PAM Matrices is a Markov process. In Analysis of the Dayhoff Model, each amino acid site in a protein can change at any time to any of the other 20 amino acids with probabilities GIVEN by the PAM table, and the changes that OCCUR at each site are independent of the amino acids found at other sites in the protein and depend only on the current amino acid at the site.

Correct choice is (d) This doesn’t allow making EVOLUTIONARY predictions on the basis of sequence alignments

Explanation: Optimal alignments provide useful INFORMATION to biologists concerning sequence relationships by giving the best possible information as to which characters in a sequence should be in the same column in an alignment, and which are insertions in one of the SEQUENCES (or deletions on the other). This information is important for making functional, STRUCTURAL, and evolutionary predictions on the basis of sequence alignments.

The correct option is (b) Gap PENALTY is added for each gap that has been introduced

Best explanation: Dynamic programming algorithms use gap PENALTIES to maximize the biological meaning. The open penalty is always applied at the START of the gap, and then the other GAPS FOLLOWING it is given with a gap extension penalty which will be less compared to the open penalty. Typical values are –12 for gap opening, and –4 for gap extension.

The CORRECT choice is (c) If the residues are not same, the mismatch score is assumed as 3

The explanation is: If the residues are not same, the mismatch score is assumed as -3 and it has to be negative. HOWEVER, these SCORES are not unique, they can be user DEFINED also, but the mismatch and gap penalty should be the negative values.

Correct ANSWER is (c) SEQUENCE LENGTH

To elaborate: In the algorithm provided by WATERMAN, the score of the alignment of random or unrelated sequences grows proportionally to the length of the sequences. However, these values are of limited use because they are based on a simple GAP scoring system.

The correct choice is (d) Needleman-Wunsch algorithm

Explanation: LOCAL alignment can be DISTINGUISHED on two broad approaches, Smith-Waterman algorithm and word methods, also KNOWN as k-tuple methods and they are implemented in the well-known families of PROGRAMS FASTA and BLAST.

The correct option is (b) two

For EXPLANATION I would say: In CONSTRUCTING a probability matrix, it allows multiple starting alignments and does not assume that there are motifs in every sequence. ALSO, the computation is a two-step procedure that INCLUDES generation of sequence motif and finding HIGHEST score.

Right answer is (B) The procedure stops prematurely if the scores reach convergence

To explain: The FINAL result is SENSITIVE to the initial alignment. The LOCAL optimum is actually a drawback of EM method. It is same as the fact that the procedure stops prematurely if the scores reach convergence.

Correct answer is (b) 1970

For explanation: NEEDLEMAN and Wunsch were among the first to DESCRIBE dynamic programming algorithm for global SEQUENCE. In global sequence alignment, an attempt to align the entirety of TWO different sequences is made, up to and including the ends of sequences.

Correct choice is (d) The method can be USEFUL in ALIGNING protein sequences to protein sequences only

The BEST I can explain: The method can be useful in aligning nucleotide to protein sequences as WELL. These programs first perform pair-wise alignment on each pair of sequences. Then, they perform local re-arrangements on these results, in ORDER to optimize overlaps between multiple sequences.

Correct answer is (c) Current versions of ProDom are built using a novel procedure based on recursive BLAST SEARCHES

The best I can explain: Current versions of ProDom are built using a novel procedure based on recursive PSI-BLAST searches and not just BLAST searches. And PRINTS is INDEED a compendium of protein fingerprints. A fingerprint is a group of CONSERVED motifs used to characterise a protein family; its diagnostic power is refined by ITERATIVE scanning of UniProt.

Right option is (a) 2 intersecting diagonal lines at the MIDPOINT

To elaborate: For perfectly aligned sequences there is a diagonal formation of dot plot. For PALINDROMIC sequences i. E. for sequences that are SYMMETRICAL from the midpoint of the sequence, there exist 2 intersecting diagonals on the plot.

Right choice is (a) They are made up of ONE secondary structure

To elaborate: PROTEIN domains are made up of two or more MOTIFS i.e. the secondary structure to form stable and folded 3-D structures. They are conserved PART of the protein sequence and can evolve, function, and exist independently of the rest of the protein chain.

The correct answer is (d) Leucine zipper

To EXPLAIN I WOULD say: Leucine zipper is associated with gene regulation and contains alpha helix with leucine at every 7th AMINO acid. While rest of them are under one of the largest families of dimerizing TRANSCRIPTION factors.