Bioinformatics Mcqs

Page No. 6

Among the following which one is not the approach to the local alignment?


aSmith-Waterman algorithm


b K-tuple method


c Words method


dNeedleman-Wunsch algorithm



Which of the following is untrue regarding the gap penalty used in dynamic programming?


aGap penalty is subtracted for each gap that has been introduced


b Gap penalty is added for each gap that has been introduced


c The gap score defines a penalty given to alignment when we have insertion or deletion


dGap open and gap extension has been introduced when there are continuous gaps (five or more)



Which of the following does not describe BLOSUM matrices?


a It stands for BLOcks SUbstitution Matrix


bIt was developed by Henikoff and Henikoff


cThe year it was developed was 1992


d These matrices are logarithmic identity values



Local alignments are more used when _____________


aThere are totally similar and equal length sequences


bDissimilar sequences are suspected to contain regions of similarity


cSimilar sequence motif with larger sequence context


dPartially similar, different length and conserved region containing sequences



Which of the following does not describe local alignment algorithm?


aScore can be negative


bNegative


cFirst row and first column are set to 0 in initialization step


dIn traceback step, beginning is with the highest score, it ends when 0 is encountered


View Answer Score can be negative

Which of the following does not describe local alignment?


aA local alignment aligns a substring of the query sequence to a substring of the target sequence


bA local alignment is defined by maximizing the alignment score, so that deleting a column from either end would reduce the score, and adding further columns at either end would also reduce the score


cLocal alignments have terminal gaps


d The substrings to be examined may be all of one or both sequences; if all of both are included then the local alignment is also global



When did Smith–Waterman first describe the algorithm for local alignment?


a1950


b1970


c1981


d1925


View Answer 1981

______ is an interactive program for generating sequence logos.


aEMBOSS


bWebLogo


cLOGOLY


d BLAST


View Answer WebLogo

Conserved positions have _____ residues and bigger symbols.


afewer


b more


cmaximum


dminimum


View Answer fewer

The overall height of a logo position reflects how conserved the position is, and the _____ of each letter in a position reflects the _______ of the residue in the alignment


aheight, relative frequency


bwidth, relative frequency


c height, amplitude


dwidth, amplitude



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