Practice Bioinformatics Written Test Multiple Choice Questions Quiz-1

Q.1

a) The genomes of most organisms are derived by vertical transmission, the inheritance of chromosomes from parents to offspring from one generation to the next
b) It is the acquisition of genetic material from a different organism
c) The transferred material becomes a temporary addition to the recipient genome
d) An extreme example is the proposed endosymbiont origin of mitochondria in eukaryotic cells and chloroplasts in plants

Q.2

a) The problem of deciding which sequences to include in the same group or cluster and which to separate into different groups or clusters is a recurring one
b) Divergence is necessary, but the sequences chosen should be clearly related based on inspection of each pair-wise alignment and a statistical analysis
c) The conservative approach is to group distinct sequences
d) The adventurous approach is to choose a set of marginally alignable sequences to pursue the difficult task of making a multiple sequence alignment and then to make profile models that may recognize divergence but will also give false predictions

Q.3

a) Using the protein from one of the organisms to search the proteome of the other for high-scoring matches should identify the ortholog as the highest- scoring match, or best hit
b) When entire proteomes of the two organisms are available, orthologs may be identified
c) a pair of orthologous genes in two organisms share so much sequence similarity that they may be assumed to have arisen from a common ancestor gene
d) each of the orthologs belongs to a family composed of paralogous sequences but irrelevant or not related to each other

Q.4

a) Paralogs may include a best hit or a high-scoring match of one of the sequences by another, but the reciprocal match can have low similarity that does not have to be significant
b) Paralogs defined by sets of three matching sequences in the selected organisms were kept separated from the clusters
c) Orthologous pairs were first defined by the best hits in reciprocal searches
d) To produce COGs, similarity searches were performed among the proteomes of phylogenetically distinct clades of prokaryotes

Q.5

a) ESTs are single DNA sequence reads that contain a small fraction of incorrect base assessments, insertions, and deletions
b) Many sequences arise from near the 5’ end of the mRNA, although every effort is usually made to read as far 3’ as possible into the upstream portion of the cDNA
c) EST libraries are useful for preliminary identification of genes by database similarity searches
d) An EST database of an organism can be analyzed for the presence of gene families,

Q.6

a) Searches of EST databases for matches to a query sequence routinely produce minimal amounts of output that must be searched manually for significant hits
b) ESTs with a high percent identity with the query sequence, a long alignment with the query sequence, and a very low E value of the alignment score represent groups of paralogous and orthologous genes
c) To identify orthologs as the most closely related sequence, ESTs were aligned using the amino acid alignment as a guide
d) To identify orthologs as the most closely related sequence, a phylogenetic tree was produced by the maximum likelihood method

Q.7

a) Gene identification of predicted proteins in the genome is designed to discover the metabolic features of an organism
b) In a particular organism or group of organisms, one particular domain can be expanded to perform a particular function
c) Comparison of the domain content of an entire proteome with that of another proteome cannot help in revealing the biological roles of diverse domains in different organisms
d) Different proteins are mosaics of domains that occur in different combinations in a given protein

Q.8

a) The method involves database similarity searches of the SwissProt database with human, worm, yeast, or E. coli genes and identification of matches with sequences from a different phylum than the query sequence
b) An analysis of ACRs that predate the radiation of the major animal phyla some 580–540 million years ago suggested that 50–60% of coding sequences are ACRs
c) These ACRs may represent proteins present at the time of the prokaryotic–eukaryotic divergence
d) Phylogenetically diverse groups of organisms have been analyzed for the presence of conserved proteins and protein domains that have been conserved over long periods of evolutionary time, called ancient conserved regions or ACRs

Q.9

a) It is a significant source of genome variation in bacteria, allowing them to exploit new environments
b) Such transfer is rendered possible by a variety of natural mechanisms in bacteria for transferring DNA from one species to another
c) Detection of HT is made possible by the fact that each genome of each bacterial species has a unique base composition
d) The time of transfer of DNA cannot be estimated by the composition of the HT DNA

Q.10