Bioinformatics Mcqs

Page No. 9

Which of the following is not a site on internet for alignment of sequence pairs?


aBLASTX


bBLASTN


cSIM


dBCM Search Launcher


View Answer BLASTX

Which of the following is not a description of dynamic programming algorithm?


aA method of sequence alignment


bA method that can take gaps into account


c A method that requires a manageable number of comparisons


dThis method doesn’t provide an optimal (This method doesn’t provide an optimal (highest scoring) alignmentscoring) alignment



Gaps are added to the alignment because it ______


aincreases the matching of identical amino acids at subsequent portions in the alignment


b increases the matching of or dissimilar amino acids at subsequent portions in the alignment


creduces the overall score


d enhances the area of the sequences



The higher is the score in the alignment _________


a the more significant is the alignmen


bor the less it resembles alignments in related proteins


cthe less significant is the alignment


dthe less it aligns with the related protein sequence



The matrices PAM250 and BLOSUM62 contain _______


apositive and negative values


b positive values only


cnegative values only


dneither positive nor negative values, just the percentage



After the derivation, the outputs of the dynamic programming are the ratios are called even scores.


a True


bfalse


ceither true and false


dnone of these


View Answer False

Use of the dynamic programming method requires a scoring system for the comparison of symbol pairs, and a scheme for GAP penalties.


aTrue


bFalse


ceither true and false


dnone of these


View Answer True

In case of the varying alignment, penalizing gaps heavily might occur. Then the best scoring local alignment between the sequences will be one that optimizes the score between matches and mismatches, without any gaps.


aTrue


bFalse


ceither true and false


dnone of these


View Answer True

Dayhoff, 1978- 1983, devised a second method for testing the relatedness of two protein sequences that can accommodate some local variation. Where this method is useful?


aFor finding repeated regions within a sequence


b For finding similar regions that are in a different order in two sequences


c For finding small conserved region such as an active site


dFor finding huge regions within sequences



The GCG alignment programs have a RANDOMIZATION option, which shuffles the second sequence and calculates similarity scores between the unshuffled sequence and each of the shuffled copies.


a True


bFalse


ceither true and false


dnone of these


View Answer True

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