Bioinformatics Practice Test 8

1. To increase the specificity of prediction, a unique feature of eukaryotic promoter is employed, which is the presence of CpG islands.

True

False

2. The ______ is an ongoing community-wide experiment on the comparative evaluation of protein-protein docking for structure prediction.

Chronological Assessment of Prediction of Interactions (CAPRI)

Critical Assessment of Prediction of Interactions (CAPRI)

Chronological Assignment of Prediction of Interactions (CAPRI)

Critical Assignment of Prediction of Interactions (CAPRI)

3. Shine-Delgarno sequence, which is a stretch of purine-rich sequence complementary to 16S rRNA in the ribosome.

False

True

4. There was little degree of success in docking an antibody-antigen complex in the second challenge for the protein-protein docking evaluation.

True

False

5. In practical circumstances there exists an experimental structure of the complex.

True

False

6. Because different prediction programs have different levels of sensitivity and specificity, it makes sense to combine results of multiple programs based on consensus. This idea has prompted development of consensus-based algorithms.

True

False

7. Which of the following is incorrect regarding the Prediction for Eukaryotes?

The consensus patterns are only derived from bioinformatics studies

The ab initio method for predicting eukaryotic promoters and regulatory elements relies on searching the input sequences for matching of consensus patterns of known promoters and regulatory elements

The consensus patterns are derived from experimentally determined DNA binding sites

The experimentally determined DNA binding sites are compiled into profiles and stored in a database for scanning an unknown sequence to find similar conserved patterns

8. Most vertebrate genes use __________ as the translation start codon and have a uniquely conserved flanking sequence call a Kozak sequence (CCGCCATGG).

AAG

AUG

AGG

ATG

9. The main issue in prediction of eukaryotic genes is the identification of exons, introns, and splicing sites.

False

True

10. Which of the following is untrue about SGP-1?

It is a similarity-based web program that aligns two genomic DNA sequences from distinctly related organisms

The near-perfect matches at the protein level define coding regions

It stands for Syntenic Gene Prediction

The program translates all potential exons in each sequence and does pair wise alignment for the translated protein sequences using a dynamic programming approach