Bioinformatics Mcqs

Page No. 5

Which of the following is untrue regarding the scoring system used in dynamic programming?


aIf the residues are same in both the sequences the match score is assumed as +5 which is added to the diagonally positioned cell of the current cell


bIf the residues are not same, the mismatch score is assumed as -3


cIf the residues are not same, the mismatch score is assumed as 3


dThe score should be added to the diagonally positioned cell of the current cell



Which of the following does not describe PAM matrices?


aThese matrices are used in optimal alignment scoring


b It stands for Point Altered Mutations


cIt stands for Point Accepted Mutations


dIt was first developed by Margaret Dayhoff



Which of the following does not describe global alignment algorithm?


a In initialization step, the first row and first column are subject to gap penalty


bScore can be negative


c In trace back step, beginning is with the cell at the lower right of the matrix and it ends at top left cell


dFirst row and first column are set to zero



Which of the following is not a disadvantage of Needleman-Wunsch algorithm?


a This method is comparatively slow


bThere is a need of intensive memory


cThis cannot be applied on genome sized sequences


dThis method can be applied to even large sized sequences



Which of the following is not an advantage of Needleman-Wunsch algorithm?


a New algorithmic improvements as well as increasing computer capacity make it possible to align a query sequence against a large DB in a few min


b Similar sequence region is of same order and orientation


cThis does not help in determining evolutionary relationship


dIf you have 2 genes that are already understood as closely related, then this type of algorithm can be used to understand them in further details



Which of the following does not describe dynamic programming?


aThe approach compares every pair of characters in the two sequences and generates an alignment, which is the best or optimal


bGlobal alignment algorithm is based on this method


cLocal alignment algorithm is based on this method


dThe method can be useful in aligning protein sequences to protein sequences only



When did Needleman-Wunsch first describe the algorithm for global alignment?


a1899


b1970


c1930


d1950


View Answer 1970

Which of the following is untrue regarding BLAST and FASTA?


aFASTA is faster than BLAST


bFASTA is the most accurate


c BLAST has limited choices of databases


dFASTA is more sensitive for DNA-DNA comparisons



Which of the following does not describe BLAST?


a It stands for Basic Local Alignment Search Tool


b It uses word matching like FASTA


c It is one of the tools of the NCBI


dEven if no words are similar, there is an alignment to be considered



Which of the following does not describe k-tuple methods?


ak-tuple methods are best known for their implementation in the database search tools FASTA and the BLAST family


b They are also known as words methods


cThey are basically heuristic methods to find local alignment


dThey are useful in small scale databases



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