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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,)
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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/8/4/2019 01 Introduction Database
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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
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http://www.nig.ac.jp
h // bl
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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
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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.html8/4/2019 01 Introduction Database
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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
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