PRIMARY & SECONDARY DATABASES BY:- PUNEET KULYANA

1. INTRODUCTION
TO DATABASES
By:-
 PUNEET
 NEERAJ
 KARTIK
 VARUN
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2. INDEX/CONTENTS
 Introduction
 Data & Information
 Database
 Biological Databases
 Types of Databases
- Primary Databases
- Secondary Databases
- Composite Databases
 References
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3. INTRODUCTION 3

4. DATA & INFORMATION
DATA
Data is raw, unorganized facts that need to
be processed.
Example:- Each student's test score is one
piece of data.
INFORMATION
When data is processed, organized,
structured or presented in a given context
so as to make it useful, it is called
information.
Example:- The average score of a class
or of the entire school is information that
can be derived from the given data.
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5. DATA INFORMATION
Definition
(Oxford
Dictionaries)
Facts and statistics collected
together for reference or
analysis
Facts provided or
learned about something
or someone
Data as processed,
stored, or transmitted
by a computer
Refers to Raw Data Analyzed Data
Description
Qualitative Or Quantitative
Variables that can be used to
make ideas or conclusions
A group of data which
carries news and
meaning
In the form of
Numbers, letters, or a set of
characters.
Ideas and inferences
Collected via
Measurements, experiments,
etc.
Linking data and making
inferences
Represented in
A structure, such as tabular
data, data tree, a data graph,
etc.
Language, ideas, and
thoughts based on the
data
Interrelation Information that is collected
Data that has been
processed
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6. S. No. Type of data Example(s) Weblinks
1. Sequence of
biomolecules viz., DNA,
RNA, proteins
GenBank, EMBL,
DDBJ, Swiss-Prot,
PIR
(i) www.ncbi.nlm.nih.gov/genba
nk/
(ii) https://www.ebi.ac.uk/embl/
(iii) www.ddbj.nig.ac.jp/
(iv)http://web.expasy.org/docs/s
wiss-prot_guideline.html
(v) http://pir.georgetown.edu/
2. Bio-molecular
structures
PDB http://www.rcsb.org/pdb/home
/home.do
3. Bibliography/scientific
literature **
PubMed, Scopus
(Search engine)
(i) www.ncbi.nlm.nih.gov/pubme
d
(ii) www.scopus.com
4. Patent databases USPTO www.uspto.gov/
5. Metabolic pathways /
molecular interactions
KEGG http://www.genome.jp/kegg/pa
thway.htm
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TYPES OF DATA & INFORMATION
Databases are categorized based on the data type. A few examples are
listed below:-

7. DATABASE???
A database is a
collection of data
in an organized
manner, which is
accessible in
various ways.
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8. WHAT ARE THE BIOLOGICAL
DATABASES ???
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9. Biological Databases serve a critical purpose in the collation
and organization of data related to biological systems.
They provide a computational support and a user-friendly
interface to a researcher for a meaningful analysis of biological
data.
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10. TYPES OF DATABASES
 Primary Databases
 Secondary Databases
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11. PRIMARY DATABASES
 Contains bio-molecular data in its original form.
 Experimental results are submitted directly into the
database by researchers, and the data are essentially
archival in nature.
 Once given a database accession number, the data in
primary databases are never changed.
 Examples :- GenBank, EMBL and DDBJ for DNA/RNA
sequences, SWISS-PROT and PIR for protein sequences
and PDB for molecular structures.
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12. GenBank
Database from NCBI, includes sequences from publicly
available resources.
http://www.ncbi.nlm.nih.gov/genbank/ 12

13. EMBL
 European Molecular Biological Laboratory
 Nucleic acid database from EBI (European
Bioinformatics Institute)
 Produced in collaboration with DDBJ and GenBank
 Search engine – SRS (Sequence Retrieval System)
http://www.ebi.ac.uk/
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14. DDBJ
 DNA Databank of Japan
 Started in 1986 in collaboration with GenBank
 Produced and maintained at NIG (National Institute
of Genetics)
http://www.ddbj.nig.ac.jp/ 14

15. SWISS PROT
 Annotated sequence database established in 1986
 Consists of sequence entries of different lie formats
 Similar format to EMBL
 http://us.expasy.org/sprot/sprot-top.html
http://www.ebi.ac.uk/uniprot/
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16. PIR
 Protein Information Resource
 A division of National Biomedical Research
Foundation (NBRF) in U.S.
 One can search for entries or do sequence similarity
search at PIR site.
http://pir.georgetown.edu/ 16

17. TrEMBL
 Translated European Molecular Biology Laboratory
 Computer annotated supplement of SWISS PROT.
 Contains all the translations of EMBL nucleotide
sequence entries not yet integrated in SWISS PROT.
http://www.ebi.ac.uk/trembl/ 17

18. COMPOSITE DATABASES
 Collection of various primary database sequences
 Renders sequence searching highly efficient as it
searches multiple resources
 Examples :- NRDB (Non Redundant Database), OWL,
MIPSX, SWISS PROT + TrEMBL
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19. 19

20. SECONDARY DATABASES
 Contains data derived from the results of analysing
primary data
 Manually created or automatically generated
 Contains more relevant and useful information
structured to specific requirements
 Example :- PROSITE, PRINTS, BLOCKS, Pfam
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21. SECONDARY DATABASES
SECONDARY
DATABASE
PRIMARY
SOURCE
INFORMATION
STORED
PROSITE SWISS PROT
Regular
expression
BLOCKS
PROSITE/PRIN
TS
Aligned
motifs(blocks)
PRINTS
OWL
(Composite DB)
Aligned motifs
Pfam SWISS PROT
Hidden Markov
Models
Profile SWISS PROT
Weighted
Matrices(profile)
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22. PROSITE
Families of proteins
Can search using regular expressions
Similar to unix commands using
wildcards, etc.
E.g., [AC]-x-V-x(4)-{ED}
Interpreted as:
[Ala or Cys]-any-Val-any-any-any-
any-{any but Glu or Asp}
Families exhibit these patterns
So we can search over families
http://ca.expasy.org/prosite/ 22

23. BLOCKS
 Motifs/blocks
are created
by
automatically
detecting the
most
conserved
regions of
each protein
family.
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24. PRINTS
 Most protein families are characterized not by one,
but by several conserved motifs
 Fingerprints are groups of conserved motifs excised
from sequence alignments
 Taken together, they provide diagnostic family
signatures. They are the basis of the PRINTS
database, and are stored in the form of aligned
motifs.
 Input about protein families is done manually
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25. Pfam
Maintained by the Sanger Centre (Cambridge)
Protein families aligned using HMMs
Hidden Markov Models
Given a new sequence
Find families which the sequence might fit into
Sequence Coverage
11912 families
Split into Pfam-A (high quality) and Pfam-B (low quality)
http://pfam.sanger.ac.uk/ 25

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27. PRIMARY VS SECONDARY DATABASES 27

28. REFERENCES
 Class notes
 ESSENTIAL BIOINFORMATICS- Jin Xiong
 file:///C:/Users/student/Downloads/DATABASES%2
0IN%20BIOINFORMATICS.pdf
 https://www.ebi.ac.uk/training/online/course/bioinfor
matics-terrified/what-database/relational-
databases/primary-and-secondary-databases
 http://www.diffen.com/difference/Data_vs_Informa
tion
 Google images
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