Gene Prediction in Eukaryotes MCQ

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• Because different prediction programs have different levels of sensitivity and specificity, it makes sense to combine results of multiple programs based on consensus. This idea has prompted development of consensus-based algorithms.
  ক

  True

  খ

  False
• TwinScan is also a similarity-based gene-finding Server and it is similar to GenomeScan in that it uses GenScan to predict all possible exons from the genomic sequence.
  ক

  True

  খ

  False
• Which of the following is untrue about SGP-1?
  ক

  The program translates all potential exons in each sequence and does pair wise alignment for the translated protein sequences using a dynamic programming approach

  খ

  The near-perfect matches at the protein level define coding regions

  গ

  It is a similarity-based web program that aligns two genomic DNA sequences from distinctly related organisms

  ঘ

  It stands for Syntenic Gene Prediction
• Which of the following is untrue about EST2Genome?
  ক

  It is a web-based program purely based on the sequence alignment approach to define intron–exon boundaries

  খ

  It compares an EST (or cDNA) sequence with a genomic DNA sequence containing the corresponding gene

  গ

  The alignment is rarely done using a dynamic programming–based algorithm

  ঘ

  Advantage of the approach is the ability to find very small exons and alternatively spliced exons that are very difficult to predict by any ab initio–type algorithms
• GenomeScan is a web-based server that combines GENSCAN prediction results with BLASTX similarity searches.
  ক

  True

  খ

  False
• The drawback of Homology-based approach is its reliance on the presence of homologs in databases.
  ক

  True

  খ

  False
• Which of the following is untrue about Homology-Based Programs?
  ক

  They are based on the fact that exon structures and exon sequences of related species are less conserved

  খ

  This approach assumes that the database sequences are correct

  গ

  It is a reasonable assumption in light of the fact that many homologous sequences to be compared with are derived from cDNA or expressed sequence tags (ESTs) of the same species

  ঘ

  Potential coding frames in a query sequence are translated and used to align with closest protein homologs found in databases
• Which of the following wrong about HMM GENE?
  ক

  It is also an HMM-based web program

  খ

  It uses a criterion called the conditional maximum likelihood to discriminate coding from non-coding features

  গ

  HMM prediction is unbiased toward the locked region

  ঘ

  If a sequence already has a sub-region identified as coding region, which may be based on similarity with cDNAs or proteins in a database, these regions are locked as coding regions
• GENSCAN is awebbased program that makes predictions based on fifth-order HMMs.
  ক

  True

  খ

  False
• Which of the following is untrue about FGENES?
  ক

  It stands for FindGenes

  খ

  It is a web-based program that uses LDA

  গ

  It is used to determine whether a signal is an exon

  ঘ

  It does not make a use of HMMs
• Which of the following is untrue about Prediction Using Discriminant Analysis for Gene Prediction?
  ক

  QDA draws a curved line based on a quadratic function

  খ

  LDA works by drawing a diagonal line that best separates coding signals from noncoding signals based on knowledge learned from training data sets of known gene structures

  গ

  Some gene prediction algorithms rely on discriminant analysis, either LDA or quadratic discriminant analysis (QDA), to improve accuracy

  ঘ

  LDA works by plotting a three-dimensional graph of coding signals versus all potential 3’ splice site positions
• GRAIL is a web-based program that is based on a neural network algorithm Which is trained on several statistical features such as splice junctions, start and stop codons, poly-A sites, promoters, and CpG islands.
  ক

  True

  খ

  False
• Which of the following is untrue about Prediction Using Neural Networks for Gene Prediction?
  ক

  A neural network is constructed with multiple layers; the input, output, and hidden layers

  খ

  The input is the gene sequence with intron and exon signals

  গ

  The model is not fed with a sequence of known gene structure

  ঘ

  The output is the probability of an exon structure
• Which of the following is untrue about PredictionUsing NeuralNetworks for Gene Prediction?
  ক

  A neural network is a statistical model with a special architecture for pattern recognition and classification

  খ

  It is composed of a network of mathematical variables

  গ

  They resembles ab initio approaches

  ঘ

  The variables in NeuralNetworks resemble the biological nervous system, with variables or nodes connected by weighted functions that are analogous to synapses
• In Ab Initio–Based Programs for Gene Prediction– Gene content refers to coding statistics, which includes nonrandom nucleotide distribution, amino acid distribution, synonymous codon usage, and hexamer frequencies.
  ক

  True

  খ

  False
• Which of the following is untrue about Ab Initio–Based Programs for Gene Prediction?
  ক

  The goal of the ab initio gene prediction programs is to discriminate exons from noncoding sequences

  খ

  The goal is joining exons together in the correct order

  গ

  The main difficulty is correct identification of exons

  ঘ

  To predict exons, the algorithms rely solely on gene signals
• Most vertebrate genes use __________ as the translation start codon and have a uniquely conserved flanking sequence call a Kozak sequence (CCGCCATGG).
  ক

  AAG

  খ

  ATG

  গ

  AUG

  ঘ

  AGG
• The main issue in prediction of eukaryotic genes is the identification of exons, introns, and splicing sites.
  ক

  True

  খ

  False
• Which of the following is untrue about translation and transcription?
  ক

  The first is capping is at the 5’ end of the transcript which involves methylation at the initial residue of the RNA

  খ

  The splicing process involves a large RNA-protein complex called spliceosome

  গ

  The second event is splicing, which is the process of removing exons and joining introns

  ঘ

  The second event is splicing, which is the process of removing introns and joining exons
• Which of the following is untrue?
  ক

  Eukaryotic nuclear genomes are much larger than prokaryotic ones

  খ

  They tend to have a very high gene density

  গ

  Eukaryotic nuclear genomes’ sizes range from 10 Mbp to 670 Gbp (1 Gbp = 109 bp)

  ঘ

  They tend to have a very high gene density