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Everything you need to know about bioinformatics. Some of the most frequently asked questions are as follows:-
Q.1. Where is the EMBL situated?
Ans: The European Molecular Biology Laboratory is situated in Heidelberg, Germany.
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Q.2. What is FASTA?
Ans: An alignment tool for protein sequences created by Pearson and Lipman in 1988.
Q.3 . What is Fish?
Ans: FISH (Fluorescence in situ hybridization) is a method, which is used to pinpoint the location of a DNA sequence on a chromosome.
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Q.4. How is HMM useful in bioinformatics?
Ans: HMM (Hidden Markov Model) is a compute, algorithm which locates features which can distinguish a protein or gene family by analyzing a range of known sequences from the family.
Q.5. What is a biological database?
Ans: A biological database is a large, organized body of persistent data, usually associated with computerized software’s designed to update queries and retrieve components of the dam stored within the system.
Q.6. Which types of biological data are stored in biological databases?
Ans: In general, biological database is a complex structure of many individual types of databases, collectively known as biological database and comprises nucleotide sequences, nucleotide structures, gene expressions data, protein structures, protein functions, metabolic pathways, cell type, cell signaling, tissues type, organs and organism type.
Q.7. What are the main properties of a good database?
Ans: A good database has following qualities:
a. Broad coverage of the chosen topic,
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b. Up-to-date information gathering,
c. Support staff,
d. Commitment to the future, and
e. Having good query interface.
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Q.8. What is the main function of biological databases?
Ans: There are two main functions of biological databases,
a. Provide biological data for research purpose to scientists,
b. To make biological data available in computer readable form.
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Q.9. In which year, first biological sequence database was published?
Ans: It was Atlas of Protein sequences and structure by Margaret Dayhoff and colleagues, published in the year 1965.
Q.10. How many sub databases are contained in nucleotide databases?
Ans: Nucleotide databases contain a lot of sub databases but there are mainly 13 databases which m-e used as DNA/RNA database such as Genebank, EMBL, DDBJ, Genomic database Yeast database, E. coil database, Specialized Database, ESTs database, STSs database, Kabat database, EPD database and REPBASE database etc.
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Q.11. Name a few protein databases?
Ans: These are: Swiss-Prot, PIR, TREMBL, GenPept, Kabatpro, Alu, PDB etc.
Q.12. What is PROSITE?
Ans: It is a database of protein motifs. This database is very useful, which provides a list of distinct structural motifs in proteins.
Q.13. Which type of information is present in GDB?
Ans: GDB is a genome database, which contains mapping information of the human genome project. It also contains a huge information about locations of genes, DNA segments, expressed sequences tags, clinical phenotypes, alleles information, and probes information.
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Q.14. Define the following.
Ans: a. ALA mode: It is an environment for building models of ligand and monomer molecular components.
b. NDB: It is the nucleic acid database.
c. HotMolecBase: This is a database having extensive information about biological factors, proteins, and genes.
Q.15. What is the microbiological database?
Ans: Microbiological database is a listing of all published microbial genomes and chromosomes such as LakeLadoga.
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Q.16. What is the virological database?
Ans: It is a database which comprises all type of viruses which infect all types of living beings such as vertebrates, invertebrates, protozoa, plants, bacteria, fungi, archaea and algae.
Q.17. Write the main properties, which are used to classify viruses in virological database?
Ans: There are many properties of viruses, which are used to classify viruses in virological database such as, virion properties, physiochemical and physical properties, genome type, proteins, G+C ratio, lipids type and biological properties.
Q.18. What is the primary database?
Ans: A database consisting of data derived experimentally such as nucleotide sequences and three- dimensional structures are known as primary databases.
Q.19. What are secondary databases?
Ans: Those data that are derived from the analysis or treatment of primary data such as secondary structures, hydrophobicity plots, and domains are stored in secondary database.
Q.20 .Name the few websites important for bioinformatics?
Ans: a. NCBI: http://www(dot)ncbi(dot)nlm.nih.gov
b. EBI: http://www(dot)ebi(dot)ac(dot)uk
c. DISC: http.7/www(dot)dna(dot)affrc(dot)go(dot)jp
d. ExPASy-SwissProt and TrEMBL: http://www(dot)expasv(dot)ch
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e. SwissProt, TrEMBL and PIR: http://www(dot)ebi(dot)ac(dot)uk
f. NCBI-Entrez (for searching sequence database): http://www(dot)ncbi(dot)nlm(dot)nih(dot)gOv/entrez/g. PDB: http://www(dot)rcsb(dot)org/pdb/
h. BLAST: http://www(dot)ncbi(dot)nlm(dot)nih(dot)gov/BLAST/
Q.21. What is EMBL?
Ans: The EMBL is the European Molecular Biology Laboratory, nucleotide sequence database, which is maintained by the European Bioinformatics Institute in Hinxton, Cambridge.
Q.22. Which institute maintains the Gene Bank?
Ans: The Gene Bank is a nucleotide database, which is maintained by the National Center for Biotechnology Information (NCBI).
Q.23. What is DDBJ?
Ans: It is the DNA Databank of Japan, which is run by the National Institute of Genetics of Japan.
Q.24. What is SGD?
Ans: The Saccharomyces genome database is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae.
Q.25. What is SWISSPROT and how is it useful?
Ans: SWISSPROT is a protein sequence database, which strives to provide a high level of annotations such as description of the function of a protein, its domain structure, protein, and nucleic acid data, post-translational modifications etc.
Q.26. What is PIR?
Ans: The protein information resources (PIR) is a division of the National Biomedical Research Foundation (NBRF) in the US.
