Bioinformatics Trends in Taxomony (MCQ)

Q1. Which of the following is not a section in the UniProt database?

     a.UniProtKB

     b. UniRef

     c.Unicode

     d. UniParc

Q2. What is the  primary purpose of the UniProtKB/Swiss-Prot section?

  a. Strong raw sequence data 

  b. Providing manually curated protein information.

  c. Containing only computationally annoted sequences.

  d. Providing RNA sequence data.

Q3. Which BLAST program is used to compare a protein query against a protein database?

  a.BLASTn

 b.BLASTp

 c.BLASTx

 d. tBLASTn

Q4.Which version of BLAST is best suited for comparing a nucleotide sequence to a translated protein database?

a.BLASTp

b.BLASTn

c.tBLASTx

d.BLASTx

Q5. In BLAST ,what does the E-Value represent?

 a. The number of exact matches in the alignment.

 b.The probability of obtaining a match by chance.

 c. The evolutionary distance between sequences.

 d.The length of the query sequence.

Q6. ThebProsite database is primarily used for identifying which of the following?

a. Protein motifs and domains

b. Secondary structure of protein.

c.3D protein structure.

d.Genetic variations.

Q7.Which type of patterns are used in prosite to identify functional sites in proteins?

 a.Phylogenetic trees.

 b. BLAST alignments.

 c. Regular expressions and profiles.

 d. HiddenMarkov Models.

Q8.Which of the primary difference between SCOP  and CATH classification systems?

a.CATH only classifies alpha helices,while SCOP classifies all proteins.

b.SCOP is used only for DNA sequences.

c.SCOP is hierarchical,whereas CATH is not.

d.SCOP is manually curated,while CATH use both manual and automated methods.

Q9.In the CATH classification system,what does "C" stand for?

a. Clustering

b.Conserved domain

c.Class

d.Complex

Q10. Which algorithm is not commonly used used for constructing Phylogenetic trees?

  a. Maximum Parsimony

  b. Hidden Markov Model.

  c. Neighbor Joining.

  d. Maximum Likelihood.

Q11. In Phylogenetics, bootstrapping is used to:

a. Align sequences in multiple sequence 

b.Identify conserved motifs

c. Model protein -ligand interactions

d.Test the reliability of branches in a Phylogenetic tree

Q12. Which of the following  is not a feature of a MEGA software?

a. Sequence alignment.

b. Phylogenetic tree construction 

c. Protein docking simulations

d. Evolutionary analysis

Q13. Molecular docking is primarily used to:

 a.Predict protein secondary structure.

b. Identify gene mutations

c. Model interactions between a ligand and a target protein.

d. Construct Phylogenetic trees

Q14.Which of the following scoring functions is commonly used in molecular docking?

a.E value

b.Binding free energy

c. GC content

d.Percent identity

15.PyRx is a virtual screening tool that mainly uses which docking software?

a.AutoDock and AutoDock Vina

b. BLAST and HMMER 

c. SCOP and CATH 

d. PhyML and MEGA 

Q16.Which file format is typically used to store ligand structures in PyRx ?

a.FASTA

b.PDBQT

c.GenBank

d.Newick

Q17.What is the purpose of RMSD (Root Mean Square Deviation)in docking studies?

a.Measure sequence similarity

b. Determine protein stability in simulation.

c. Quantify structural deviation between docked poses

d.Align Phylogenetic trees

Q18.Which of the following is not a molecular docking method?

a. Rigid docking

b. Flexible docking

c. Hidden Markov docking

d.Molecular dynamics docking

Q19. Which database provides structural information of biomolecules?

a.KEGG

b.PDB

c.GeneBank

d.RefSeq

Q20. Which parameter in BLAST output indicates the percentage of identical residues in an alignment?

a.Bit Score

b.Query Coverage

c.Percent Identify 

d. E-Value

Answer: 1-c,2-b,3-b,4-d,5-b,6-a,7-c,8-d,9-c,10-b,11-d,12-c,13-c,14-b,15-a,16-b,17-c,18-c,19-b,20-c.