Bioinformatics Mcqs

Page No. 90

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.


a PubChem

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bGenbank

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c MeSH

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d SwissProt

✓


View Answer SwissProt

Which of the given statement is incorrect about Orthologs?


aIn 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

✖


bTo 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

✓


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

✖


dOrthologs 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

✖


View Answer 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

Which of the given statement is incorrect about Clusters of functionally related genes?


aIn 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

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

✓


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

✖


dThe function of a particular gene can sometimes be predicted, given the known function of a neighboring, closely linked gene

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

Evolutionary modeling can include various types of analyses. Which is mostly not one of them?


aThe prediction of chromosomal rearrangements

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bEu/Hetero-chromatin structures

✓


cDuplications at gene, chromosomal and full genome level

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dDuplications at the protein domain level

✖


View Answer Eu/Hetero-chromatin structures

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 _______


aXPBLAST

✓


bWU-BLAST

✖


cBLAST

✖


dFASTA

✖


View Answer XPBLAST

Which of the given statement is incorrect about proteome analyses?


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

✖


bDue 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

✖


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

✖


dBLAST does not give statistical evaluation of alignment scores

✓


View Answer BLAST does not give statistical evaluation of alignment scores

. The all-against-all analyses provide an indication as to the number of protein/gene families in an organism. This number represents the core proteome of the organism from which all biological functions have diversified.


aTrue

✓


bFalse

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ceither true and false

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dnone of the mentioned

✖


View Answer True

Which of the given statements is incorrect about Clustering by single linkage?


aIn First step, a group of related sequences found in the all-against-all proteome comparison is subjected to a multiple sequence alignment usually by CLUSTALW

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b A neighbor-joining algorithm is rarely used in this method

✓


cThis procedure and the algorithms are the same as those used to make a phylogenetic tree by the distance methods

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dA distance matrix that shows the number of amino acid changes between each pair of sequences is made

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View Answer A neighbor-joining algorithm is rarely used in this method

Which of the given statements is incorrect about Clustering by making subgraphs?


aEach sequence is a vertex and each pair of sequences that is matched with a significant alignment score is joined by an edge that is weighted according to the statistical significance of the alignment score

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bOne way to identify the most strongly supported clusters is simply to add the most weakly supported edges in the graph

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cOne way to identify the most strongly supported clusters is simply to remove the most weakly supported edges in the graph

✓


dAn edge is weighted according to the statistical significance of the alignment score

✖


View Answer One way to identify the most strongly supported clusters is simply to remove the most weakly supported edges in the graph

Which of the given statements is incorrect about Cluster analysis?


aClustering organizes the proteins into groups by some objective criterion

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bOne criterion for a matching protein pair is the statistical significance of their alignment score

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cThe P or E value from BLAST searches cannot be the criterion for a matching protein pair

✓


dA criterion for clustering proteins is the distance between each pair of sequences in a multiple sequence alignment

✖


View Answer The P or E value from BLAST searches cannot be the criterion for a matching protein pair

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