Which of the given statement is incorrect about proteome analyses?
a) For BLAST, setting an effective database size appropriate for each search and program is important
b) 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
c) BLAST is used for obtaining a correct statistical evaluation of alignment scores
d) BLAST does not give statistical evaluation of alignment scores
Q.2.
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 _______
a) XPBLAST
b) WU-BLAST
c) BLAST
d) FASTA
Q.3.
Evolutionary modeling can include various types of analyses. Which is mostly not one of them?
a) The prediction of chromosomal rearrangements
b) Eu/Hetero-chromatin structures
c) Duplications at gene, chromosomal and full genome level
d) Duplications at the protein domain level
Q.4.
Which of the given statement is incorrect about Clusters of functionally related genes?
a) 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
b) In related organisms, gene order on the chromosome is least likely to be conserved
c) As the relationship between the organisms decreases, local groups of genes remain clustered together, but chromosomal rearrangements move the clusters to other locations
d) The function of a particular gene can sometimes be predicted, given the known function of a neighboring, closely linked gene
Q.5.
Which of the given statement is incorrect about Orthologs?
a) 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
b) 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
c) The best hit in each proteome is likely to be with an ortholog of the query gene
d) 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
Q.6.
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<for the alignment score and an alignment that includes 60–of the query sequence are generally required in order to avoid matches to paralogs.
a) PubChem
b) Genbank
c) MeSH
d) SwissProt
Q.7.
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.
a) True
b) False
Q.8.
Processed pseudogenes are also derived from a functional gene and they contain introns and a promoter.
a) True
b) False
Q.9.
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.
a) True
b) False
Q.10.
New gene functions are thought to be gained by duplication of an existing gene creating two tandem copies.
a) True
b) False
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