This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “Sequence – Based Approaches”.
1. Which of the following is untrue regarding expressed sequence tags (ESTs)?
a) One of the high throughput approaches to genome-wide profiling of gene expression is sequencing ESTs
b) They are short sequences obtained from cDNA clones
c) They serve as short identifiers of full-length genes
d) They are typically in the range of 800 to 900 nucleotides in length
View Answer
Explanation: ESTs are typically in the range of 200 to 400 nucleotides in length obtained from either the 5’end or 3’end of cDNA inserts. Libraries of cDNA clones are prepared through reverse transcription of isolated mRNA populations by using oligo (dT) primers that hybridize with the poly (A) tail of mRNAs and ligation of the cDNAs to cloning vectors.
2. To generate EST data, clones in the cDNA library are randomly selected for sequencing from either end of the inserts.
a) True
b) False
View Answer
Explanation: The EST data are able to provide a rough estimate of genes that are actively expressed in a genome under a particular physiological condition. This is because the frequencies for particular ESTs reflect the abundance of the corresponding mRNA in a cell, which corresponds to the levels of gene expression at that condition. Another potential benefit of EST sampling is that, by randomly sequencing cDNA clones, it is possible to discover new genes.
3. Which of the following is untrue regarding the drawbacks of expressed sequence tags (ESTs)?
a) They are often of lowquality because they are automatically generated without verification
b) Many bases are ambiguously determined, represented by N’s
c) Frame shift errors and artifactual stop codons are some common errors
d) Despite of all the failures, the translation the sequences is smooth
View Answer
Explanation: Common errors also include frameshift errors and artifactual stop codons, resulting in failures of translating the sequences. In addition, there is often contamination by vector sequence, introns (fromunspliced RNAs), ribosomal RNA (rRNA), mitochondrial RNA, among others. ESTs represent only partial sequences of genes.
4. It has been estimated that up to 11% of cDNA clones may be chimeric.
a) True
b) False
View Answer
Explanation: A problem of ESTs is the presence of chimeric clones owing to cloning artifacts in library construction, in which more than one transcript is ligated in a clone resulting in the 5_ end of a sequence representing one gene and the 3’ end another gene. Another fundamental problem with EST profiling is that it predominantly represents highly expressed, abundant transcripts. Weakly expressed genes are hardly found in a EST sequencing survey.
5. Which of the following is untrue regarding expressed sequence tags (ESTs)?
a) EST libraries can be easily generated from various cell lines, tissues, organs, and at various developmental stages
b) Although individual ESTs are prone to error, an entire collection of ESTs contains valuable information
c) Identification of cDNA clone is difficult
d) ESTs can also facilitate the unique identification of a gene from a cDNA library
View Answer
Explanation: A short tag can lead to a cDNA clone. Often, after consolidation of multiple EST sequences, a full-length cDNA can be derived. By searching a non-redundant EST collection, one can identify potential genes of interest.
6. GenBank has a special EST database, dbEST that contains EST collections for a large number of organisms.
a) True
b) False
View Answer
Explanation: The rapid accumulation of EST sequences has prompted the establishment of public and private databases to archive the data. The mentioned database is regularly updated to reflect the progress of various EST sequencing projects. Each newly submitted EST sequence is subject to a database search. If a strong similarity to a known gene is found, it is annotated accordingly.
7. Which of the following is untrue regarding EST Index Construction?
a) The goal of the EST databases is to organize and consolidate the largely redundant EST data
b) The process includes a preprocessing step that removes masks repeats
c) There is no screening of vector contaminants
d) The goal of the EST databases is to improve the quality of the sequence information so the data can be used to extract full-length cDNAs
View Answer
Explanation: The process includes a preprocessing step that removes vector contaminants and masks repeats. Vecscreen, can be used to screen out bacterial vector sequences. This is followed by a clustering step that associates EST sequences with unique genes.
8. Which of the following is untrue regarding UniGene?
a) It is an NCBI EST cluster database
b) Overlapping EST sequences are computationally processed to represent a single expressed gene
c) Each cluster is a set of overlapping EST sequences
d) The overlapping EST sequences are computationally processed to represent a set of expressed genes
View Answer
Explanation: The database is constructed based on combined information from dbEST, GenBank mRNA database, and “electronically spliced” genomic DNA. Only ESTs with 3’poly-A ends are clustered to minimize the problem of chimerism. The resulting 3’EST sequences provide more unique representation of the transcripts.
9. Which of the following is untrue regarding TIGR Gene Indices?
a) It is an EST database that the similar type of clustering method from UniGene
b) It is an EST database that uses a different clustering method from UniGene
c) It compiles data from dbEST, GenBank mRNA and genomic DNA data, and TIGR’s own sequence databased Sequences are only clustered if they are more than 95% identical for over a fortynucleotide region in pairwise comparisons
d) None of the mentioned
View Answer
Explanation: BLAST and FASTA are used to identify sequence overlaps. In the sequence assembly stage, both TIGR Assembler and CAP3 are used to construct contigs, producing a so-called tentative consensus (TC). To prevent chimerism, transcripts are clustered only if they match fully with known genes.
10. Which of the following is untrue regarding SAGE?
a) It stands for Serial analysis of gene expression
b) It is another high throughput, sequence-based approach for global gene expression profile analysis
c) It stands for Squared analysis of gene expression
d) Unlike EST sampling, SAGE is more quantitative in determining mRNA expression in a cell
View Answer
Explanation: In this method, short fragments of DNA (usually 15 base pairs [bp]) are excised from cDNA sequences and used as unique markers of the gene transcripts. The sequence fragments are termed tags. They are subsequently concatenated (linked together), cloned, and sequenced.
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