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Sequence and Structure Databases (GATE)

Description: GAte NEt SLet
Number of Questions: 15
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Tags: GAte NEt SLet Sequence and Structure Databases
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Which of the following is a pair of signal transduction pathway databases?

  1. Reactome and MANET

  2. Netpath and MetaCyc

  3. Netpath and MANET

  4. Reactome and MetaCyc

  5. Reactome and NetPath


Correct Option: E
Explanation:

Correct answer. NetPath is a manually curated resource of human signal transduction pathways. Reactome is a navigable map of human biological pathways, ranging from metabolic processes (metabolic pathways) to hormonal signalling (signal transduction pathways).

Which of the following databases contains protein domain families generated from the UniProtKB database by automated sequence comparisons?

  1. TIGRFAMs database

  2. Pfam database

  3. ProDom database

  4. Kyoto database

  5. MUMmer database


Correct Option: C
Explanation:

The ProDom database contains protein domain families generated from the UniProtKB database by automated sequence comparisons.

Which among the following is a DNA and protein sequence alignment software package?

  1. FASTA

  2. GtRNAdb

  3. ClustalW2

  4. MetaCyc

  5. Melanie


Correct Option: A
Explanation:

Correct answer. FASTA is a DNA and protein sequence alignment software package.

Which of the following are examples of secondary databases?

  1. SWISS-PROT
  2. PROSITE
  3. Genbank
  4. Pfam
  1. 1 and 2

  2. 1 and 3

  3. 2 and 3

  4. 2 and 4

  5. 3 and 4


Correct Option: D
Explanation:

Correct answer. Secondary databases contain results from the analysis of sequences in the primary databases. Examples of secondary databases are PROSITE and Pfam.

Which of the following are examples of DNA and protein sequence alignment programs?

  1. ClustalW2
  2. FASTA
  3. Melanie
  4. PROSITE
  1. 1 and 2

  2. 1 and 3

  3. 1 and 4

  4. 2 and 3

  5. 2 and 4


Correct Option: C
Explanation:

Correct answer. ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins. PROSITE is a protein database consisting of entries describing the protein families, domains and functional sites as well as amino acid patterns and profiles in them.

Which of the following databases of protein families includes their annotations and multiple sequence alignments generated using hidden Markov models?

  1. InterPro

  2. Swiss-Prot

  3. UniParc

  4. Pfam

  5. CAZy


Correct Option: D
Explanation:

Correct answer. Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models.

Which of the following are examples of protein-protein interaction databases?

P. BioGRID Q. STRING R. Reactome S. SignaLink 2.0

  1. P and Q

  2. P and R

  3. P and S

  4. Q and R

  5. R and S


Correct Option: A
Explanation:

Correct answer. The Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database of protein-protein and genetic interactions. STRING is a database of known and predicted protein interactions.

Which of the following is a curated biological database of protein-protein and genetic interactions?

  1. BioGRID

  2. TRANSFAC

  3. PDB

  4. TrEMBL

  5. Pfam


Correct Option: A
Explanation:

Correct answer. The Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database of protein-protein and genetic interactions.

Which among the following is a Bioinformatics Resource Center dedicated to providing data to the scientific community for human pathogens?

  1. TIGRFAMs

  2. ProDom

  3. PRINTS

  4. VectorBase

  5. GenBank


Correct Option: D
Explanation:

Correct answer. VectorBase is an NIAID Bioinformatics Resource Center dedicated to providing data to the scientific community for Invertebrate Vectors of Human Pathogens.

__________ is a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank sequence database.

  1. Sequin

  2. EMBL

  3. BioOne

  4. Embase

  5. PDB


Correct Option: A
Explanation:

Correct answer. Sequin is a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank sequence database.

Match the column – I with column – II and select the correct option.

 
Column – I Column – II
A. BRAEMBL 1. National Institute of Genetics
B. DDBJ 2. European Bioinformatics Institute
C. ENA 3. National Center for Biotechnology Information
D. GenBank 4. University of Queensland
  1. A - 2, B - 1, C - 4, D - 3

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

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

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

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


Correct Option: C
Explanation:

Correct answer. BRAEMBL, pronounced "bramble", is a research support facility for bioinformatics services at the University of Queensland. The European Nucleotide Archive (ENA) is a repository providing free and unrestricted access to annotated DNA and RNA sequences produced and maintained by the European Bioinformatics Institute. The DNA Data Bank of Japan (DDBJ) is a biological database that collects DNA sequences located at the National Institute of Genetics (NIG) in the Shizuoka prefecture of Japan. The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations produced and maintained by the National Center for Biotechnology Information (NCBI).

Which of the following is an example of evolutionary database?

  1. BOINC

  2. SIMAP

  3. TreeFam

  4. InterPro

  5. ModBase


Correct Option: C
Explanation:

Correct answer. TreeFam is a database of evolutionary trees of animal genes which aims at developing a curated resource that gives reliable information about ortholog and paralog assignments, and evolutionary history of various gene families.

The International Nucleotide Sequence Database (INSD) consists of

  1. DNA Data Bank of Japan
  2. European Nucleotide Archive
  3. GenBank
  4. PROSITE
  5. VectorBase
  1. 1, 2 and 3

  2. 1, 3 and 5

  3. 2, 3 and 4

  4. 2, 4 and 5

  5. 3, 4 and 5


Correct Option: A
Explanation:

Correct answer. The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences. It consists of the following databases: DNA Data Bank of Japan (Japan), GenBank (USA) and the European Nucleotide Archive (UK).

Match the column – I with column – II and select the correct option.

 
Column – I Column – II
A. PROSITE 1. University of Geneva
B. PDB 2. Brookhaven National Laboratory
C. OMIM 3. John Hopkins University
  1. A - 1, B - 2, C - 3

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

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

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

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


Correct Option: A
Explanation:

Correct answer. The PROSITE dictionary of sites and patterns in proteins is prepared by Amos Bairoch at the University of Geneva. The X-ray crystallography Protein Data Bank (PDB) is compiled at the Brookhaven National Laboratory. Online Mendelian Inheritance in Man (OMIM) data bank is prepared by Victor Mc Kusick, Claire A. Francomano and Stylianos E. Antonarakis at John Hopkins University.

Match the column – I with column – II and select the correct option.

 
Column – I Column – II
A. DDBJ 1. Bibliographic database
B. MEDLINE 2. Nucleotide sequence database
C. NatureServe 3. Model organism database
D. WormBase 4. Biodiversity database
  1. A - 4, B - 3, C - 2, D - 1

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

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

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

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


Correct Option: C
Explanation:

Correct answer. DNA Data Bank of Japan (DDBJ) is a nucleotide sequence database. It is a biological database that collects DNA sequences. MEDLINE is a bibliographic database of life sciences and biomedical information which provides bibliographic information for articles from academic journals covering medicine, nursing, pharmacy, dentistry, veterinary medicine and health care. NatureServe is a sophisticated biodiversity database which acts as an authoritative source for information on more than 70,000 plants, animals and ecosystems of the United States and Canada. WormBase is an online biological database about the biology and genome of the model organism Caenorhabditis elegans (a nematode) and contains information about other related nematodes.

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