01 Introduction Database

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Introduction toBIOINFORMATICS


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What is Bioinformatics?

The marriage between biology and informatics


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Understanding natures mute elegant language of living cells the question of modern molecular biology.

From an alphabet of only four letters representing the chemic

subunits of DNA, emerges a syntax of life processes whosmost complex expression is man.

The unravelling and use of this alphabet to form new wordand phrases is a central focus of the field of molecular biology

The staggering volume of molecular data and its cryptic ansubtle patterns have led to an absolute requirement focomputerized databases and analysis tools.

The challenge is in finding new approaches to deal with thvolume and complexity of data, and in providing researchers wit

better access to analysis and computing tools in order tadvance understanding of our genetic legacy and its role health and diseases.From the National Centre for Biotechnology Information (NCBI), http:://www.ncbi.nlm.nih.gov


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Essentially, Bioinformatics has three component

The creation of databases allowing the storage andmanagement of large biological data sets.

The development of algorithms and statistics todetermine relationships among members of large

data sets. The use of these tools for the analysis and

interpretation of various types of biological data,including DNA, RNA and protein sequences, proteinstructures, gene expression profiles, andbiochemical pathways


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Data Jungle

Structuralbiology

MolecularBiology

Genetics

Medicine

Sequencinginformation

PhysiologyToxicologyGene

Expression

From: EBI SRS tutorial


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DATABASE: a collection of data that has a regularstructure and that is organized in such a way that acomputer can easily find and retrieve information.

A database is generally a collection of RECORDS,available through specific entries, each of whichcontains one or more FIELD.

RECORD

ID Locus Sequence

FIELDS

ID=Unique identifier


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Factors that made bioinformaticsso important

Rapid and cheap techniques for DNAsequencing

The development of powerful computers

Internet and the Wide World Web


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DATA SOURCES FOR DATABASES

Direct scientific submission

Genome sequencing labs and groups

Scientific literature

Patent applications


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Bioinformatics Developers

They develop tools for bioinformatics Experts in Mathematics, Statistics and Informatics Computational biologists

Bioinformatics Users

They use the tools of bioinformatics Researchers (Biologists, Biotechnologist,)


11/30Introduction to Bioinformatics: www.bioinformatics.com/courses.com/bioinfom

Genes, Proteins, RNA.

Complete genomes

Biochemical pathways & processes

Cellular & developmental processes

Tissue & organism physiology

Ecological processes & populations

Biological complexity

COMPL

EXITY


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Nucleic Acid Sequences

Protein Sequences

Database Retrieval

Database Retrieval

Sequencing ProjectManagement

Nucleic Acid SequenceAnalysisDNA/RNA Folding

RestrictionMapping

Seeking Coding regions

Translation to aminoacids

Protein Sequence analysis

Prediction of Function

DatabaseSimilarity

Searching

Pair wiseSequenceComparison

MultipleSequenceAlignment

Phylogeny Structure prediction

Structure analysis

Motifs and Patterns


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USANCBI (National Center for Biotechnology Information

http://www.ncbi.nlm.nih.gov/

Europe

EBI (European Bioinformatics Institute,Hinxton, UK)

http://www.ebi.ac.uk/

Japan

NIG (National Institute of Genetics)

Sites where the integration among databases

and between databases and software is develope

http://www.nig.ac.jp/index-e.htmlLink rete
http://www.ncbi.nlm.nih.gov/http://www.ebi.ac.uk/http://www.ebi.ac.uk/http://www.ebi.ac.uk/http://www.ebi.ac.uk/http://www.ebi.ac.uk/http://www.ebi.ac.uk/http://www.ebi.ac.uk/http://www.ebi.ac.uk/http://www.ncbi.nlm.nih.gov/


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Biological database history

1965

M. Dayhoff et al. published Atlas of Protein Sequences andStrucures

1982

EMBL started the DNA sequence collection

1983Genbank started the DNA sequence collection

1984

DNA sequence databases of Japan

1988

Embl/GenBank/DDBJ agreed on common format for dataelements


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GenBank

DDBJEMBL

EMBL

Entrez

SRS

GetentryNIG

CIB

NCBI

SubmissionsUpdates Submissions

Updates

SubmissionsUpdates

The International Sequence Database Collaboratio

EBI

NCBI

http://www nig ac jp
http://www.nig.ac.jp/http://www.nig.ac.jp/


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http://www.nig.ac.jp

h // bl
http://www.nig.ac.jp/http://www.nig.ac.jp/


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http://www.embl.org


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NCBI

National Center for BiotechnologyInformation

National Library of Medicine

Bethesda, MD


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NCBI: The National Center for Biotechnology Information

Created by US Congress in 1988, NCBI is part ofthe National Library of Medicine at NationaInstitutes of Health.

Bethesda,Maryland


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The National Center for Biotechnology Information


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The National Center for Biotechnology Information(NCBI)

Created as a part of the National Library of

Medicinein 1988 Establish public databases Research in computational biology Develop software tools for sequence analysis Disseminate biomedical information

Tools: BLAST(1990), Entrez (1992)

GenBank (1992)

Free MEDLINE (PubMed, 1997)

Other databases: dbEST, dbGSS, dbSTS, MMDB,OMIM, UniGene, GeneMap, Taxonomy, CGAP,SAGE, Gene, RefSeq


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http://www.ncbi.nlm.nih.gov/Sitemap/index.html
http://www.ncbi.nlm.nih.gov/Sitemap/index.htmlhttp://www.ncbi.nlm.nih.gov/Sitemap/index.html


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Databases connections

http://www.ncbi.nlm.nih.gov/

Database/datamodel/index.html

Entrez databases and the connections between them
http://www.ncbi.nlm.nih.gov/Database/datamodel/index.htmlhttp://www.ncbi.nlm.nih.gov/Database/datamodel/index.htmlhttp://www.ncbi.nlm.nih.gov/Database/datamodel/index.htmlhttp://www.ncbi.nlm.nih.gov/Database/datamodel/index.htmlhttp://www.ncbi.nlm.nih.gov/Database/datamodel/index.htmlhttp://www.ncbi.nlm.nih.gov/Database/datamodel/index.htmlhttp://www.ncbi.nlm.nih.gov/Database/datamodel/index.html


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Entrez data ases and the connect ons etween them

http://www.ncbi.nlm.nih.gov/Database/datamodel/index.html Link re
http://www.ncbi.nlm.nih.gov/Database/datamodel/index.htmlhttp://www.ncbi.nlm.nih.gov/Database/datamodel/index.html


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01 Introduction Database

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