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Lecture 2 Introduction To The Computational Tools

The document discusses important web servers and databases for computational biology. It describes the functions and goals of key servers such as NCBI, EBI, DDBJ, Swiss-Prot/ExPASy, and PDB. It also discusses the international collaboration on nucleotide sequence databases between GenBank, EMBL, and DDBJ. Finally, it covers general topics about biological databases including their structure, features, types based on data source and type, and maintenance status.

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Bhawna Rathi
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18 views

Lecture 2 Introduction To The Computational Tools

The document discusses important web servers and databases for computational biology. It describes the functions and goals of key servers such as NCBI, EBI, DDBJ, Swiss-Prot/ExPASy, and PDB. It also discusses the international collaboration on nucleotide sequence databases between GenBank, EMBL, and DDBJ. Finally, it covers general topics about biological databases including their structure, features, types based on data source and type, and maintenance status.

Uploaded by

Bhawna Rathi
Copyright
© © All Rights Reserved
Available Formats
Download as PPTX, PDF, TXT or read online on Scribd
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Topic Name - Introduction to the

computational tools and servers


• NCBI (The National Center for
Biotechnology Information;
IMPORTANT – http://www.ncbi.nlm.nih.gov/
WEB SERVERS • EBI (The European Bioinformatics
WITH Institute)
– http://www.ebi.ac.uk/
MULTIPLE
• DDBJ (DNA Data Bank of Japan)
APPLICATIONS – http://www.ddbj.nig.ac.jp/index-e
.html
• SwissProt/ExPASy (Swiss Bioinformatics
Resource)
– http://expasy.cbr.nrc.ca/sprot/
• PDB (The Protein Databank)
– http://www.rcsb.org/PDB/
INTERNATIONAL NUCLEOTIDE
SEQUENCE DATABASE COLLABORATION
GQuery
NIH
NCBI
•Submissions
•Updates
GenBank
EMBL
•Submissions
EMBL •Updates

DDBJ
CIB EBI

NIG •Submissions
•Updates
SRS
getentry
NCBI SERVER

Created in 1988 as a part of the


National Library of Medicine at NIH
– Establish public databases
– Research in computational biology
– Develop software tools for sequence analysis
– Disseminate biomedical information
NCBI SERVER
EMBL-EBI SERVER

•GOALS:
• To provide freely available data and
bioinformatics services to all facets
of the scientific community
• To contribute to the advancement of
biology through basic investigator-
driven research
• To provide advanced bioinformatics
training to scientists at all levels
• To help disseminate cutting-edge
technologies to industry
EMBL-EBI SERVER
• DDBJ Center is officially certified to collect nucleotide
sequences from researchers and to issue the
internationally recognized accession number to data

DDBJ submitters.
• The accession number issued for each sequence data is
unique on the database and internationally recognized to
guarantee the submitter the property of the submitted
and published data.
EXPASY
PROTEIN DATA BANK
• Structured collection of information.

• Consists of basic units called


records or entries.

• Each record consists of fields,


WHAT ARE which hold pre-defined data related
to the record.
DATABASES?
• For example, a protein database
would have protein entries as
records and protein properties as
fields (e.g., name of protein, length,
amino-acid sequence)
• Comprehensive, but easy to search.

CHIEF • Annotated, but not “too annotated”.

FEATURES • A simple, easy to understand structure.


OF • Cross-referenced.
BIOLOGICAL
DATABASE • Minimum redundancy.

• Easy retrieval of data.


 Based on Data Source:
• Primary Databases
- Original submissions by experimentalists
- Content controlled by the submitter
- Examples: GenBank, DDBJ, EMBL
• Secondary Databases
TYPES OF - Derived from primary data
- Examples: NCBI Protein, Refseq, TPA,
BIOLOGICAL RefSNP, GEO datasets, UniGene,
DATABASES Homologene, Structure, Conserved
Domain
• Specialized Databases
- Contains information belonging to a
specific category only.
- Examples: HUGO, HGMD
 Based on Data Type:
• Genome Databases: Flybase, HPRD
etc.
• Sequence Databases
- Nucleotide: GENBANK, EMBL, DDBJ
TYPES OF - Protein: GENPEPT, UNIPROT
BIOLOGICAL • Structure Databases: PDB, MMDB
• Microarray Databases: GEO, Array
DATABASES
Express
• Chemical Databases: Pubchem
• Pathway Databases: KEGG, BRINDA
• Literature Databases: PUBMED,
MEDLINE
 Based on Maintenance status:
• NCBI
• EMBL
• DDBJ
TYPES OF
 Based on Data Access:
BIOLOGICAL • Publicly Available
DATABASES • Available with copyright
• Browsing only
• Academic use

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