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Bioinformatics

Description: Bioinformatics Sequence and Structure DatabasesBioinformaticsGenomics and Proteomics
Number of Questions: 15
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Tags: Bioinformatics Sequence and Structure Databases Genomics and Proteomics
Attempted 0/15 Correct 0 Score 0

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


Correct Option: D
Explanation:

The blastx tool compares translated nucleotide query sequence against translated nucleotide databases.

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


Correct Option: A
Explanation:

RDP provides quality-controlled, aligned and annotated Bacterial and Archaeal 16S rRNA sequences and Fungal 28S rRNA sequences and a suite of analysis tools to the scientific community. SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya).

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


Correct Option: B
Explanation:

DiProDB is a database designed to collect and analyse thermodynamic, structural and other dinucleotide properties.

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


Correct Option: B
Explanation:

It is correct. Both P and R are enzyme database. REBASE is a database of information about restriction enzymes and DNA methyltransferases. BRENDA (BRaunschweig ENzyme DAtabase) is an enzyme information system representing one of the most comprehensive enzyme repositories.

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


Correct Option: C
Explanation:

Yes, it is the correct answer. ExPASy stands for Expert Protein Analysis System.

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


Correct Option: A
Explanation:

It is correct answer as it is not matched correctly. PAUP stands for Phylogenetic Analysis Using Parsimony.

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


Correct Option: C
Explanation:

It is correct. Both the statements are false. Pfam-A and Pfam-B is automatically generated from the PRODOM database. Dot-matrix representations denote the sequence as the coordinates of a two-dimensional graph.

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


Correct Option: E
Explanation:

Yes, it is correct. Single-letter codes used by FASTA for aspartic acid is D.

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


Correct Option: C
Explanation:

It is the correct answer. Both are false. PAM matrices are based on Dayhoff model of protein evolution. The paired dot in the sequence alignment represents conserved substitutions.

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


Correct Option: E
Explanation:

Yes, this is the correct answer. Both statements are true. A tree representation of a family showing the relationships between members and the pattern of inheritance of a given trait is known as pedigree. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) is a distance-based method in tree construction.

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

  1. PDBsum

  2. BMRB

  3. MMDB

  4. FSSP

  5. RasMol


Correct Option: B
Explanation:

Yes, it is the correct answer. Biological Magnetic Resonance Bank (BMRB) is a database for NMR spectroscopy information on biomolecules hosted at the University of Wisconsin at Madison.

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

 
Column – I
Column – II
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


Correct Option: C
Explanation:

Yes, it is correctly matched. RGD (Rat Genome Database): Genomic and phenotype data for Rattus norvegicus RegulonDB: A model of the complex regulation of transcription initiation or regulatory network of the cell Escherichia coli K-12 Wormbase: Genome of the model organism Caenorhabditis elegans Flybase: Genome of the model organism Drosophila melanogaster

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

 
Column - I
Column - II
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


Correct Option: A
Explanation:

Yes, it is the correct answer. Single-letter codes used by FASTA for glutamine, tryptophan, arginine and lysine are Q, W, R and K respectively.

Match the entries in column I and column II

 
Column - I
Column - II
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


Correct Option: D
Explanation:

Yes, it is the correct answer. PDB is a primary protein structure database. SCOP is a secondary protein structure database. UniSTS is a complementary DNA database. Entrez is a bibliographic database.

Match the entries in column - I and column - II

 
Column - I
Column - II
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


Correct Option: D
Explanation:

It is correct answer. ICTVdb classifies viruses based primarily on their chemical characteristics, genomic type, nucleic acid replication, diseases, vectors and geographical distribution among other characteristics. It was developed at the Australian National University. Molecular Modeling Database (MMDB) is 3D Macromolecular structure resources by the National Center for Biotechnology Information (NCBI) Structure Group. Biological Magnetic Resonance Bank (BMRB) Database for NMR spectroscopy information on biomolecules hosted at the University of Wisconsin at Madison.

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