This set of Bioinformatics Questions and Answers for Campus interviews focuses on “Sequencing cDNA Libraries of Expressed Genes, Submission of Sequences to the Databases”.
1. Two common goals in sequence analysis are to identify sequences that encode proteins, which determine all cellular metabolisms, and to discover sequences that regulate the expression of genes or other cellular processes.
a) True
b) False
View Answer
Explanation: Genomic sequencing meets both goals. However, only a small percentage of the genomic sequence of many organisms actually encodes proteins because of the presence of introns within coding regions and other noncoding regions in the genome.
2. cDNA libraries have been prepared that have the same sequences as the mRNA molecules produced by organisms, or else cDNA copies are sequenced directly by RT-PCR (copying of mRNA by reverse transcriptase followed by sequencing of the cDNA copy by the polymerase chain reaction).
a) True
b) False
View Answer
Explanation: There has been a great deal of progress in developing computational methods for analyzing genomic sequences and finding these protein-encoding regions. But these methods are not completely reliable and, furthermore, such genomic sequences are often not available.
3. Using cDNA sequence with the __________ it is much simpler to locate protein-encoding sequences in these molecules.
a) exons taken out
b) exons removed
c) introns added
d) introns removed
View Answer
Explanation: The only possible difficulty is that a gene of interest may be developmentally expressed or regulated in such a way that the mRNA is not present. This problem has been circumvented by pooling mRNA preparations from tissues that express a large proportion of the genome, from a variety of tissues and developing organs or from organisms subjected to several environmental influences.
4. An important development for computational purposes was the decision by Craig Venter to prepare databases of partial sequences of the expressed genes, called expressed sequence tags or ESTs.
a) True
b) False
View Answer
Explanation: This was an important development from resolution point of view. This has just enough DNA sequence to give a good idea of the protein sequence.
5. The translated sequence can then be compared to a database of protein sequences with the hope of finding a strong similarity to a protein of known function, and hence to identify the function of the cloned EST.
a) True
b) False
View Answer
Explanation: The translated sequence can then be compared in the mentioned way hence to identify the function of the cloned EST. The corresponding cDNA clone of the gene of interest can then be obtained and the gene completely sequenced.
6. Investigators are encouraged to submit their newly obtained sequences directly to a member of the International Nucleotide Sequence Database Collaboration, such as the NCBI, DDBJ, and EMBL.
a) True
b) False
View Answer
Explanation: NCBI stands for National Center for Biotechnology Information. It manages GenBank. DDBJ and EMBL stand for DNA Database Bank of Japan and European Molecular Biology Laboratory respectively.
7. NCBI reviews new entries and updates existing ones, as requested.
a) True
b) False
View Answer
Explanation: A database accession number, which is required to publish the sequence, is provided. New sequences are exchanged daily by the GenBank, EMBL, and DDBJ databases.
8. Which of the given statements is incorrect?
a) The simplest and newest way of submitting sequences is through the Web site on a Web form page called BankIt
b) The sequence can also be annotated with information about the sequence, such as mRNA start and coding regions
c) The submitted form is transformed into GenBank format and returned to the submitter for review before being added to GenBank
d) Sequin does not run on UNIX
View Answer
Explanation: The other method of submission is to use Sequin (formerly called Authorin), which runs on personal computers and UNIX machines. The program provides an easy-to-use graphic interface and can manage large submissions such as genomic sequence information.
9. Which of the given statements is untrue?
a) There is no detailed check of sequence accuracy prior to submission to GenBank and other databases
b) Often, a sequence is submitted at the time of publication of the sequence in a journal article, providing a certain level of checking by the editorial peer review process
c) No sequence is submitted without being published or prior to publication
d) In laboratories performing large sequencing projects, such as those engaged in the Human Genome Project or the genome projects of model organisms, the granting agency requires a certain level of accuracy of the order of 1 possible error per 10 kb
View Answer
Explanation: Many sequences are submitted without being published or prior to publication. As mentioned in option d, the level of accuracy should be sufficient for most sequence analysis applications such as sequence comparisons, pattern searching, and translation.
10. Granting agency requires a certain level of accuracy in case of errors. Which of the given statements is untrue regarding it?
a) In other laboratories, such as those performing a single-attempt sequencing of ESTs, the error rate may be much higher, approximately 1 in 100, including incorrectly identified bases and inserted or deleted bases
b) Incorrect bases always translate to the right amino acid
c) Base insertions/deletions will cause frame-shifts in the sequence
d) Making alignment with a protein sequence becomes difficult because of frameshifts
View Answer
Explanation: In translating EST sequences in GenBank and other databases, incorrect bases may translate to the wrong amino acid. Another type of database sequence that is error-prone is a fragment of sequence from the immunological variant of a pathogenic organism, such as the regions in the protein coat of the human immunodeficiency virus (HIV). Although this low level of accuracy may be suitable for some purposes such as identification, for more detailed analyses, e.g., evolutionary analyses, the accuracy of such sequence fragments should be verified.
Sanfoundry Global Education & Learning Series – Bioinformatics.
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