Sequence Assembly and Gene Identification MCQ

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• New gene functions are thought to be gained by duplication of an existing gene creating two tandem copies.
  ক

  True

  খ

  False
• Pseudogenes are DNA sequences that were derived from distinct genes but which have acquired mutations that are deleterious to function in the same period of time.
  ক

  True

  খ

  False
• Processed pseudogenes are also derived from a functional gene and they contain introns and a promoter.
  ক

  True

  খ

  False
• In all-against-all self comparison, A comparison is made in which every protein is used as a query in a similarity search against a database composed of the rest of the proteome, and the significant matches are identified by a low expect value.
  ক

  True

  খ

  False
• In protein/domain analysis, each protein in the predicted proteome is again used as a query of a curated protein sequence database such as ____ in order to locate similar domains and sequences. To find orthologs, very low E value scores (E<10<20) for the alignment score and an alignment that includes 60–80% of the query sequence are generally required in order to avoid matches to paralogs.
  ক

  PubChem

  খ

  Genbank

  গ

  MeSH

  ঘ

  SwissProt
• Which of the given statement is incorrect about Orthologs?
  ক

  In comparing two proteomes, a common standard is to require that for each pair of orthologs, the first of the pair is the best hit when the second is used to query the proteome of the first

  খ

  To identify orthologs, each protein in the proteome of an organism is used as a query in a similarity search of a database comprising the proteomes of only one different organism

  গ

  The best hit in each proteome is likely to be with an ortholog of the query gene

  ঘ

  Orthologs are genes that are so highly conserved by sequence in different genomes that the proteins they encode are strongly predicted to have the same structure and function and to have arisen from a common ancestor through speciation
• Which of the given statement is incorrect about Clusters of functionally related genes?
  ক

  In microbial genomes, genes specifying a metabolic pathway may be contiguous on the genome where they are coregulated transcriptionally in an operon by a common promoter

  খ

  In related organisms, gene order on the chromosome is least likely to be conserved

  গ

  As the relationship between the organisms decreases, local groups of genes remain clustered together, but chromosomal rearrangements move the clusters to other locations

  ঘ

  The function of a particular gene can sometimes be predicted, given the known function of a neighboring, closely linked gene
• Evolutionary modeling can include various types of analyses. Which is mostly not one of them?
  ক

  The prediction of chromosomal rearrangements

  খ

  Eu/Hetero-chromatin structures

  গ

  Duplications at gene, chromosomal and full genome level

  ঘ

  Duplications at the protein domain level
• An all-against-all analysis requires first making a database of the proteome. This database is then sequentially searched by each individual protein sequence of the proteome using a rapid database similarity search tool such as _______
  ক

  XPBLAST

  খ

  WU-BLAST

  গ

  BLAST

  ঘ

  FASTA
• Which of the given statement is incorrect about proteome analyses?
  ক

  For BLAST, setting an effective database size appropriate for each search and program is important

  খ

  Due to the large number of comparisons that must be made in these types of analyses and due to the volume of program output, the procedure must be automated on a local machine using Perl scripts or a similar method and a database system

  গ

  BLAST is used for obtaining a correct statistical evaluation of alignment scores

  ঘ

  BLAST does not give statistical evaluation of alignment scores
• The higher the E value, the more significant the alignment between a pair of matching sequences.
  ক

  True

  খ

  False
• The ________ are _______ by genetic structure to retroviruses.
  ক

  STR retrotransposons, related

  খ

  LTR retrotransposons, related

  গ

  STR transposons, related

  ঘ

  LTR retrotransposons, not related
• Yeast is about ______ compact than E. coli.
  ক

  fivefold, less

  খ

  threefold, more

  গ

  twofold, less

  ঘ

  twofold, more
• _______ of the Drosophila sequence is composed of TEs and _____ is heterochromatic regions that do not include genes.
  ক

  one-fourth, one-third

  খ

  one-fifth, one-fourth

  গ

  one-sixth, one-eighth

  ঘ

  one-sixth, one-third
• In Metabolic pathways and regulation, as genes are identified in a new genome sequence, some will be found that are known to act sequentially in a metabolic pathway or to have a known role in gene regulation in other organisms.
  ক

  True

  খ

  False
• In Protein 2D gel Electrophoresis, Individual proteins produced by the genome can be separated to _____ by this method and specific ones identified by various _______
  ক

  smaller extent, biochemical and immunological tests

  খ

  a large extent, biochemical and immunological tests

  গ

  a large extent, biochemical tests only

  ঘ

  smaller extent, purely mechanical tests
• In Proteolysis and fragment sequencing, Protein spots may be excised from a two-dimensional protein gel and subjected to a combination of amino acid sequencing and cleavage analyses using the techniques of mass spectrometry and high-pressure liquid chromatography.
  ক

  True

  খ

  False
• WU-BLAST produces P scores and BLAST (NCBI) produces E scores where _________
  ক

  E = ln (1 + P2)

  খ

  E = ln (1 – P2)

  গ

  E = ln (1 + P)

  ঘ

  E = ln (1 – P)
• In the program COGNITOR each protein in the proteome is used as a query of a database of protein clusters.
  ক

  True

  খ

  False
• Which of the given statement is incorrect about the gene map?
  ক

  Gene order in two related organisms reflects the order that was present in a common ancestor genome. Chromosomal breaks followed by reassembly of fragments in a different order can produce new gene maps

  খ

  Gene order is only revealed by the physical order of genes on the chromosome

  গ

  Sequence variations (polymorphisms) that are close to (tightly linke

  ঘ

  a trait may be used to trace the trait by virtue of the fact that the polymorphism and the trait are seldom separated from one generation to the next [ These types of evolutionary changes in genomes have been modeled by computational methods
• Which of the given statement is incorrect about Functional Genomics?
  ক

  Functional genomics involves the preparation of mutant or transgenic organisms with a mutant form of a particular gene usually designed to prevent expression of the gene

  খ

  An abnormal properties of the mutant organism does not reveal the gene function

  গ

  When two or more members of a gene family are found, rather than a single match to a known gene, the biological activity of these members may be analyzed by functional genomics to look for diversification of function in the family

  ঘ

  A more detailed analysis of the relative amount of sequence variability in a chromosomal region within populations of closely related species can reveal the presence of genes that are under selection
• Which of the following information is not directly obtained by microarray analysis?
  ক

  Which genes are expressed at a particular stage of the cell cycle

  খ

  Which genes are expressed at a particular stage of developmental cycle of an organism

  গ

  Which genes are depleted at what time

  ঘ

  Genes that respond to a given environmental signal to the same extent
• Which of the given statement is incorrect?
  ক

  The predicted set of proteins for the genome is referred to as the proteome

  খ

  The amino acid sequence of proteins encoded by the predicted genes is used as a query of the protein sequence databases in a database similarity search

  গ

  A match of a predicted protein sequence to one or more database sequences serves only to identify the gene function but it doesn’t validate the gene prediction

  ঘ

  The genome sequence is annotated with the information on gene content and predicted structure, gene location, and functional predictions
• Gene identification in prokaryotic organisms is simplified by their lacking _________
  ক

  exons

  খ

  introns

  গ

  coding segments

  ঘ

  useful nucleotide sequences
• TEs (Transposable Elements) can at most comprise one-fourth of the genome sequence.
  ক

  True

  খ

  False
• In case of genome sequence assembly which of the given statement is incorrect?
  ক

  Full chromosomal sequences are assembled from the overlaps in a highly redundant set of fragments by an automatic computational method or from the fragment order on a physical map

  খ

  Chromosome cloning is carried out in bacterial artifical chromosomes (BACs)

  গ

  Chromosomes of a target organism are purified, fragmented, and subcloned in fragments of size hundreds of bp

  ঘ

  Genome sequences are assembled from DNA sequence fragments of approximate length 500 bp obtained using DNA sequencing machines
• Screening the predicted protein sequences against ______ library confirms the prediction and expression of the gene.
  ক

  expressed sequence tag (EST)

  খ

  tags

  গ

  palindromes

  ঘ

  proteomes
• Each genome sequence is scanned for protein-encoding genes using gene models trained on known gene sequences from the same organism.
  ক

  True

  খ

  False
• Sequencing of genomes depends on the assembly of a large number of DNA reads into a linear, contiguous DNA sequence.
  ক

  True

  খ

  False