Bioinformatics Mcqs

Page No. 21

In the initial step of EM algorithm, the 20-residue-long binding motif patterns in each sequence are aligned as an initial guess of the motif.


a True


bFalse


ceither true and false


dnone of these


View Answer True

In EM algorithm, as an example, suppose that there are 10 DNA sequences having very little similarity with each other, each about 100 nucleotides long and thought to contain a binding site near the middle 20 residues, based on biochemical and genetic evidence. the following steps would be used by the EM algorithm to find the most probable location of the binding sites in each of the ______ sequences.


a30


b10


c 25


d 20


View Answer 10

Out of the two repeated steps in EM algorithm, the step 2 is ________


a the maximization step


bthe minimization step


cthe optimization step


dthe normalization step



Which of the following is untrue regarding Expectation Maximization algorithm?


aAn initial guess is made as to the location and size of the site of interest in each of the sequences, and these parts of the sequence are aligned


bThe alignment provides an estimate of the base or amino acid composition of each column in the site


cThe column-by-column composition of the site already available is used to estimate the probability of finding the site at any position in each of the sequences


dThe row-by-column composition of the site already available is used to estimate the probability



The Expectation Maximization algorithm has been used to identify conserved domains in unaligned proteins only


a True


bFalse


ceither true and false


dnone f these


View Answer False

Two commonly encountered examples are the Genetics Computer Group’s MSF format and the CLUSTALW ALN format.


aTrue


bFalse


ceither true and false


dnone of the mentioned


View Answer True

MACAW is a local multiple sequence alignment program only.


aTrue


bFalse


ceither true and false


dnone of the mentioned


View Answer False

GDE (Genetic Data Environment) provides a general interface on UNIX machines for sequence analysis, sequence alignment editing, and display.


aTrue


bFalse


ceither true and false


dnone of the mentioned


View Answer True

Which of the following is not a feature of editors and formatters?


aprovision for displaying the sequence on a color monitor with residue colors to aid in a clear visual representation of the alignment


brecognition of the multiple sequence format that was output by the MSA (Multiple Sequence Alignment) program


cmaintenance of the alignment in a suitable format when the editing is completed


ddisallowing shading conserved residues in the alignment



Even if many pseudocounts are added in comparison to real sequence counts, the amino acid frequencies will not have any effect or influence.


aTrue


bFalse


ceither true and false


dnone of the mentioned


View Answer False

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