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Bioinformatics

Bioinformatics sequence and structure databases, genomics, and proteomics

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Questions

Question 1 Multiple Choice (Single Answer)

Which of the following tools compares translated nucleotide query sequence against translated nucleotide databases?

  1. Blastp
  2. Blastn
  3. TBlastn
  4. Blastx
  5. All of the above
Question 2 Multiple Choice (Single Answer)

Which of the following is a pair of RNA databases?

  1. RDP and SILVA
  2. RDP and EuroCarbDB
  3. EuroCarbDB and SILVA
  4. Reactome and SILVA
  5. RDP and Reactome
Question 3 Multiple Choice (Single Answer)

Which of the following databases is designed to collect and analyse thermodynamic, structural and other dinucleotide properties?

  1. FINDbase
  2. DiProDB
  3. GreenPhylDB
  4. TRANSFAC
  5. TreeBASE
Question 4 Multiple Choice (Single Answer)

Which of the following are enzyme databases?
P. REBASE
Q. BioGRID
R. BRENDA
S. SMPDB

  1. Only P and Q
  2. Only P and R
  3. Only P and S
  4. Only Q and R
  5. Only Q and S
Question 5 Multiple Choice (Single Answer)

Which of the following is correctly matched?

  1. SMART : Simple Modular Alignment Research Tool
  2. CDD : Conserved Domain Dictionary
  3. ExPASy : Expert Protein Analysis System
  4. PAM : Parallel Aligned Mutation
  5. SNP : Small Nucleotide Polymorphism
Question 6 Multiple Choice (Single Answer)

Which of the following pairs of 'abbreviation : full form' is mismatched?

  1. PAUP : Proteomic Analysis Using Parsimony
  2. UPGMA : Unweighted Pair Group Method with Arithmetic Mean
  3. DDD : Dali Domain Dictionary
  4. SCOP : Structural Classification of Proteins
  5. PopSet : Population Study Data Sets
Question 7 Multiple Choice (Single Answer)

Which of the following statements are FALSE?

  1. ClustalW program accepts the input sequences only in the FASTA format.
  2. Pfam-A and Pfam-B are automatically generated from the PROSITE database.
  3. Dot-matrix representations denote the sequence as the coordinates of a 3D graph.
  4. Smith-Waterman algorithm is used by local alignment.
  1. Only 1 and 2
  2. Only 1 and 4
  3. Only 2 and 3
  4. Only 2 and 4
  5. Only 3 and 4
Question 8 Multiple Choice (Single Answer)

Which of the following matches of 'amino acid and its single letter code used by FASTA' is incorrect?

  1. Phenylalanine : F
  2. Tyrosine : Y
  3. Asparagine : N
  4. Glutamic acid : E
  5. Aspartic acid : C
Question 9 Multiple Choice (Single Answer)

Which of the following statements are FALSE?
P. PAM matrices are based on Markov model of protein evolution.
Q. SRS is a website that indexes many biological databases and is searchable by keywords.
R. Sequences that share an arbitrary, threshold level of similarity determined by alignment of matching bases are termed as homologous sequences.
S. The paired dot in the sequence alignment represents semi-conserved substitutions.

  1. Only P and Q
  2. Only P and R
  3. Only P and S
  4. Only Q and R
  5. Only R and S
Question 10 Multiple Choice (Single Answer)

Which of the following statements are TRUE?
P. Maximum parsimony is not a character-based method in tree construction.
Q. A bifurcating branch point in the phylogenetic tree is known as clade.
R. Pedigree is a tree representation of a family showing the relationships between members and the pattern of inheritance of a given trait.
S. UPGMA is a distance-based method in tree construction.

  1. Only P and Q
  2. Only P and S
  3. Only Q and R
  4. Only Q and S
  5. Only R and S
Question 11 Multiple Choice (Single Answer)

Which of the following is a database for NMR spectroscopy information on biomolecules?

  1. PDBsum
  2. BMRB
  3. MMDB
  4. FSSP
  5. RasMol
Question 12 Multiple Choice (Single Answer)

Match the column – I (Genome databases) with column – II (Model organisms)

 
Column – I 
        </strong>|<strong>Column &#x2013; II</strong>|

|A. RGD|1. Escherichia coli|
|B. RegulonDB|2. Rattus norvegicus|
|C. Wormbase|3. Drosophila melanogaster|
|D. Flybase|4. Caenorhabditis elegans|

  1. A - 4, B - 3, C - 2, D - 1
  2. A - 2, B - 1, C - 3, D - 4
  3. A - 2, B - 1, C - 4, D - 3
  4. A - 3, B - 2, C - 4, D - 1
  5. A - 1, B - 2, C - 3, D - 4
Question 13 Multiple Choice (Single Answer)

Match the entries in column - I (amino acids) and column - II (their single-letter codes used by FASTA)

 
Column - I 
        </strong>|<strong>Column - II</strong>|

|P. Glutamine|1. Q|
|Q. Tryptophan|2. W|
|R. Arginine|3. R|
|S. Lysine|4. K|

  1. P - 1, Q - 2, R - 3, S - 4
  2. P - 2, Q - 1, R - 3, S - 4
  3. P - 2, Q - 3, R - 4, S - 1
  4. P - 3, Q - 4, R - 1, S - 2
  5. P - 4, Q - 3, R - 1, S - 1
Question 14 Multiple Choice (Single Answer)

Match the entries in column I and column II

 
Column - I 
        </strong>|<strong>Column - II</strong>|

|P. PDB|1. Complementary DNA database|
|Q. SCOP|2. Bibliographic database|
|R. UniSTS|3. Primary protein structure database|
|S. Entrez|4. Secondary protein structure database|

  1. P - 1, Q - 2, R - 3, S - 4
  2. P - 2, Q - 1, R - 3, S - 4
  3. P - 2, Q - 3, R - 4, S - 1
  4. P - 3, Q - 4, R - 1, S - 2
  5. P - 4, Q - 3, R - 1, S - 1
Question 15 Multiple Choice (Single Answer)

Match the entries in column - I and column - II

 
Column - I 
        </strong>|<strong>Column - II</strong>|

|A. ICTVdb|1. University of Wisconsin|
|B. MMDB|2. Australian National University|
|C. BMRB|3. National Center for Biotechnology Information|

  1. A - 1, B - 2, C - 3
  2. A - 1, B - 3, C - 1
  3. A - 2, B - 1, C - 3
  4. A - 2, B - 3, C - 1
  5. A - 3, B - 2, C - 1
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