This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “Genome Annotation”.
1. The genome annotation process involves two steps: gene prediction and functional assignment.
Explanation: Before the assembled sequence is deposited into a database, it has to be analyzed for useful biological features. The genome annotation process provides comments for the features.
2. Which of the following is incorrect regarding gene annotation?
a) The gene annotation of the human genome employs a combination of theoretical prediction and experimental verification
b) Gene structures are first predicted by ab initio exon prediction programs
c) The predicted genes are compared with experimentally determined cDNA and EST sequences
d) The pairwise alignment programs are not involved
Explanation: The predictions are verified by BLAST searches against a sequence database. The predicted genes are further compared with experimentally determined cDNA and EST sequences using the pairwise alignment programs such as GeneWise, Spidey, SIM4, and EST2 Genome.
3. Which of the following is incorrect regarding gene ontology?
a) It exists because there is a need to standardize protein functional descriptions
b) It uses a limited vocabulary to describe molecular functions
c) Biological processes are not described though
d) The cellular components are described using limited vocabulary
Explanation: The controlled vocabulary is organized such that a protein function is linked to the cellular function through a hierarchy of descriptions with increasing specificity. The top of the hierarchy provides an overall picture of the functional class, whereas the lower level in the hierarchy specifies more precisely the functional role. This way, protein functionality can be defined in a standardized and unambiguous way.
4. Which of the following is incorrect regarding gene ontology?
a) There is standardization of the names and activities
b) There is no standardization of associated pathways
c) It provides consistency in describing overall protein functions
d) It facilitates grouping of proteins of related functions
Explanation: A GO description of a protein provides three sets of information: biological process, cellular component, and molecular function, each of which uses a unique set of non-overlapping vocabularies. The standardization of the names, activities, and associated pathways provides consistency in describing overall protein functions.
5. Which of the following is incorrect regarding Automated Genome Annotation?
a) It exists because of the need to develop fast and automated methods to annotate the genomic sequences
b) The automated approach relies on homology detection
c) The automated approach doesn’t rely on heuristic sequence similarity searching
d) Automation brings speed in gene annotation process
Explanation: If a newly sequenced gene or its gene product has significant matches with a database sequence beyond a certain threshold, a transfer of functional assignment is taking place. In addition to sequence matching at the full length, detection of conserved motifs often offers additional functional clues.
6. Conserved functional sites can be identified by profile and hidden Markov model–based motif and domain search tools such as SMART and InterPro.
Explanation: Detecting remote homologs typically involves combined searches of protein motifs and domains and prediction for secondary and tertiary structures. The prediction can also be performed using structure-based approaches such as threading and fold recognition.
7. The remote homology detection helps to shed light on the possible functions of the proteins that previously have no functional information at all.
Explanation: The bioinformatic analysis can spur an important advance in knowledge in many cases. Some hypothetical proteins, because of their novel structural folds, still cannot be predicted even with the advanced bioinformatics approaches and remain challenges for both experimental and computational work.
8. Which of the following is incorrect regarding genome economy?
a) It is a phenomenon of synthesizing more proteins from fewer genes
b) This is a major strategy that eukaryotic organisms use to achieve a myriad of genotypic diversities only
c) This is a major strategy that eukaryotic organisms use to achieve a myriad of phenotypic diversities
d) There are numerous underlying genetic mechanisms to help account for genome economy
Explanation: A major mechanism responsible for the protein diversity is alternative splicing, which refers to the splicing event that joins different exons from a single gene to form different transcripts. A related mechanism, known as exon shuffling, which joins exons from different genes to generate more transcripts, is also common in eukaryotes. It is known that, in humans, about two thirds of the genes exhibit alternative splicing and exon shuffling during expression, generating 90% of the total proteins.
9. In some circumstances, one mRNA transcript can lead to the translation of more than one protein.
Explanation: For example, human dentin phosphoprotein and dentin sialoprotein are proteins involved in tooth formation. An mRNA transcript that includes coding regions from both proteins is translated into a precursor protein that is cleaved to produce two different mature proteins.
10. Which of the following is incorrect regarding GeneQuiz?
a) It is a web server for protein DNA annotation
b) It is a web server for protein sequence annotation
c) It compares a query sequence against databases using BLAST and FASTA to identify homologs with high similarities
d) It performs domain analysis using the PROSITE and Blocks databases
Explanation: It performs domain analysis using the PROSITE and Blocks databases as well as analysis of secondary structures and super-secondary structures that includes prediction of coiled coils and transmembrane helices. Multiple search and analysis results are compiled to produce a summary of protein function with an assigned confidence level (clear, tentative, marginal, and negligible).
Sanfoundry Global Education & Learning Series – Bioinformatics.
To practice all areas of Bioinformatics, here is complete set of 1000+ Multiple Choice Questions and Answers.