Biotechnology Question Bank, Database Retrieval Tools, European Molecular Biology Laboratory

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5. What are database retrieval tools and what are its uses?

  • Among the database retrieval tools are ENTREZ, taxonomy, BROWSER, Locus LINK. Entrez is an integrated database retrieval system. Through this system one can access literature (in the form of abstracts), sequences, and structures. Entrez is an excellent system for obtaining comprehensive information on a given biological question. The taxonomy browser provides information on taxonomic classification of various species.

6. Mention all the databases and the type of information available on them?

Database Information available

  • EMBL (European Molecular Biology Laboratory) Nucleotide sequence

  • SWISS-PROT Annotated protein sequence

  • PDB (Protein Database) Three-dimensional structure of proteins

  • Ribosomal RNA database rRNA subunit sequences

  • PALI database Phylogenetic analysis and alignment of proteins

7. What are the different types of sequences entered into the databases?

Based on their origin the various DNA sequence entries into the databases can be classified into the following types:

  • cDNA: Many sequences entered are originally cDNA sequences. While entering such sequences one has to mention this fact. Also, this information is available when the sequence is retrieved. Thus, these are expressed as part of the total sequences.

  • Genomic DNA: Most sequences entered are Genomic DNA sequences.ESTs: Stands for Expressed Sequence Tags. These comprises of partial cDNA clones i.e. cDNAs sequence from one end. It has its own special database called the db EST. EST data can give information regarding the expression patterns by counting the number of ESTs corresponding to each gene divided by the total number of ESTs.

  • GST: In Plasmodium falciparum the enzyme Mung Bean nuclease cuts between the genes. The digested DNA can be used to prepare genomic library. The sequence can be read from either ends as in ESTs.Organelle DNA: Eukaryotic cell possess cell organelles such as mitochondria, chloroplast. Since they possess their own DNA which is different from the Genomic DNA one has to mention it specifically while entering such data.

  • Other molecules such as tRNA and smaller RNAs are also entered into databases.

8. Write short note on the nomenclature system used in Bioinformatics work?

  • The nomenclature system that researchers use in bioinformatics work is based on the International Union of Pure and Applied Chemistry recommendations. This ensures uniformity of use across all the researchers. The main bases are represented by GATC. However, in certain experiments due to problems of sequencing the sequence identification is not clear at certain positions.

  • In such cases if the ambiguity persists such that, for instance, the nucleotide cannot be differentiated as to whether it is G or C but one can be sure it is not A or T then the symbol used is S.

  • Also, since in most organisms DNA is double stranded one might face a problem if one starts encountering symbols that mean more than one base at a given position. In certain cases, the complimentary symbols are same as in the given strand because in both the cases they mean the same set of bases.

9. How are the following bases represented?

a) guanine, (b) adenine, (c) Thymine, (d) Cytosine, (e) Purine, (f) Pyrimidine, (g) Amino, (h) Keto, (i) Strong Hydrogen bonds, (j) Weak Hydrogen bonds, (not-G, H follows G in the alphabet, (l) not-A, B follows a in the alphabet, (m) not-T (not-U), V follows U in the alphabet, (n) not-C, D follows C in the alphabet, (0) Any base.

A) Guanine, (B) Adenine, (C) Thymine, (D) Cytosine, (E) Purine, (F) Pyrimidine, (G) Amino, (H) Keto, (I) Strong Hydrogen Bonds, (J) Weak Hydrogen Bonds, (Not-G, H Follows G in the Alphabet, (L) Not-A, …
a) guanine, (b) adenine, (c) Thymine, (d) Cytosine, (e) Purine, (f) Pyrimidine, (g) Amino, (h) Keto, (i) Strong Hydrogen bonds, (j) Weak Hydrogen bonds, (not-G, H follows G in the alphabet, (l) not-A, B follows a in the alphabet, (m) not-T (not-U), V follows U in the alphabet, (n) not-C, D follows C in the alphabet, (0) Any base.

Symbol

Meaning

Base (s)

G

G

Guanine

A

A

Adenine

T

T

Thymine

C

C

Cytosine

R

G OR A

Purine

Y

T C

Pyrimidine

M

A C

Amino

K

G T

Keto

S

G C

Strong (3 Hydrogen bonds)

W

A T

Weak (2 Hydrogen bonds)

H

A C T

Not-G, H follows G in the alphabet

B

G T C

Not-A, B follows A in the alphabet

V

G C A

Not-T (not-U),V follows U in the alphabet

D

G A T

Not-C, D follows C in the alphabet

N

G A T C

Any

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