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Biological Databases

Bioinformatics is an interdisciplinary field that combines biology and informatics to analyze complex biological data using various scientific disciplines. The document highlights the historical contributions of Margaret Oakley Dayhoff, who created the first biological databases and developed the one-letter amino acid code. It also outlines important types of databases used in bioinformatics, including primary, secondary, composite, structural, pathway, interactome, and enrichment databases.

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15 views15 pages

Biological Databases

Bioinformatics is an interdisciplinary field that combines biology and informatics to analyze complex biological data using various scientific disciplines. The document highlights the historical contributions of Margaret Oakley Dayhoff, who created the first biological databases and developed the one-letter amino acid code. It also outlines important types of databases used in bioinformatics, including primary, secondary, composite, structural, pathway, interactome, and enrichment databases.

Uploaded by

blackswordsmanyuudai
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Biological

Databases
Bioinformatics Division, NIB
Created: 22.01.2023
Updated: 19.12.2024
What is Bioinformatics?

Bioinformatics = Biology + Informatics (Bengali: জব তথ্যিবজ্ঞান )

Biology = Study of living things and their vital processes

Informatics = Informatics harnesses the power and possibility of digital


technology to transform data and information into knowledge that people use
every day (https://luddy.indianapolis.iu.edu/).
…Bioinformatics is an interdisciplinary field of science that develops methods and software

tools for understanding biological data, especially when the data sets are large and complex.

Bioinformatics uses biology, chemistry, physics, computer science, computer programming,

information engineering, mathematics and statistics to analyze and interpret biological

data. The subsequent process of analyzing and interpreting data is referred to as

computational biology…. Wikipedia


It Started with Dayhoff: the first bioinformatician

IBM Punch card technology for Electrochemistry

From 1958 to 1962, she developed COMPROTEIN, ‘a complete computer program for
the IBM 7090’ designed to determine protein primary structure using Edman peptide Margaret Belle (Oakley) Dayhoff (March
sequencing data. This software, entirely coded in FORTRAN on punch-cards, is 11, 1925 – February 5, 1983)
the first occurrence of what we would call today a de novo sequence assembler
1) Dayhoff developed the one-letter
amino acid code
2) The first biological databases—
that is, the first groupings of biological
information ordered on a computer—
were produced by Margaret Oak-
ley Dayhoff

3) This one-letter code was first used in


Dayhoff and Eck’s 1965 Atlas of Protein
Sequence and Structure, the first ever
biological sequence database. The first
edition of the Atlas contained 65 protein
sequences, most of which were interspecific
variants of a handful of proteins.
Ref: 1) A brief history of bioinformatics
Jeff Gauthier, Antony T. Vincent, Steve J. Charette and Nicolas Derome
2) Hallam Stevens - Life Out of Sequence A Data-Driven History of
Bioinformatics-University Of Chicago Press (2013)
Database?…
A database is an organized collection of structured information, or
data, typically stored electronically in a computer system. A
database is usually controlled by a database management system
(DBMS). Together, the data and the DBMS, along with the
applications that are associated with them, are referred to as a
database system, often shortened to just
database….(https://www.oracle.com/)
Things we will learn…

● Types of databases

● Use of Different databases

● How to use them?

● How to collect sequences?


Why so much data?…
Classification:
Important databases:
Primary database:
1) NCBI (https://www.ncbi.nlm.nih.gov/)
2) ENA (https://www.ebi.ac.uk/ena/browser/home)
Secondary database:
1) InterPro(https://www.ebi.ac.uk/interpro/)
Composite database:
1) Uniport (https://www.uniprot.org/)
Structural database:
1) RCSB PDB (https://www.rcsb.org/)
Important databases:
Pathway database:
1) KEGG (https://www.genome.jp/)
2) Reactome (https://reactome.org/)
Interactome database:
1) STRING (https://string-db.org/)
2) GeneMANIA (https://genemania.org/)
Enrichment database:
1) DAVID Bioinformatics Database (https://david.ncifcrf.gov/home.jsp)
2) Enrichr (https://maayanlab.cloud/Enrichr/)
Let's Explore!!!

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