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Biological Databases. By : Lim Yun Ping E mail : [email protected] National University of Singapore. Overview. Introduction What is a database What type of databases can we access What roles do they play What type of information can we get from them How do we access these information.

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biological databases

Biological Databases

By : Lim Yun PingE mail : [email protected]

National University of Singapore

overview
Overview
  • Introduction
  • What is a database
  • What type of databases can we access
  • What roles do they play
  • What type of information can we get from them
  • How do we access these information
what is a database
What is a database ?
  • Convenient method of vast amount of information
  • Allows for proper storing, searching & retrieving of data.
  • Before analyzing them we need to assemble them into central, shareable resources
why databases
Why databases ?
  • Means to handle and share large volumes of biological data
  • Support large-scale analysis efforts
  • Make data access easy and updated
  • Link knowledge obtained from various fields of biology and medicine
different database types
Different Database Types
  • depends on the nature of information stored

(sequences, 2D gel or 3D structure images)

  • manner of storage (flat files, tables in a relational database, etc)
  • In this course we are concerned more about the different types of databases rather than the particular storage
features
Features
  • Most of the databases have a web-interface to search for data
  • Common mode to search is by Keywords
  • User can choose to view the data or save to your computer
  • Cross-references help to navigate from one database to another easily
types of biological databases accessible
Types Of Biological Databases Accessible

There are many different types of database but for routine sequence analysis, the following are initially the most important

  • Primary databases
  • Secondary databases
  • Composite databases
primary databases
Primary databases
  • Contain sequence data such as nucleic acid or protein
  • Example of primary databases include :

Nucleic Acid Databases

  • EMBL
  • Genbank
  • DDBJ

Protein Databases

  • SWISS-PROT
  • TREMBL
  • PIR
secondary databases
Secondary databases
  • Or sometimes known as pattern databases
  • Contain results from the analysis of the sequences in the primary databases
  • Example of secondary databases include :
  • PROSITE
  • Pfam
  • BLOCKS
  • PRINTS
composite databases
Composite databases
  • Combine different sources of primary databases.
  • Make querying and searching efficient and without the need to go to each of the primary databases.
  • Example of composite databases include :
  • NRDB – Non-Redundant DataBase
  • OWL
slide12

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

NCBI, at the NIH campus, USA

EMBL : http://www.embl-heidelberg.de/European Molecular Biology Laboratory, UK

DDBJ

DDBJ : http://www.ddbj.nig.ac.jpDNA Databank of Japan

Nucleic acid Databases

the international sequence database collaboration
The International Sequence Database Collaboration
  • These three databases have collaborated since 1982. Each database collects and processes new sequence data and relevant biological information from scientists in their region e.g. EMBL collects from Europe, GenBank from the USA.
  • These databases automatically update each other with the new sequences collected from each region, every 24 hours. The result is that they contain exactly the same information, except for any sequences that have been added in the last 24 hours.
  • This is an important consideration in your choice of database. If you need accurate and up to date information, you must search an up to date database.
amount of data grows rapidly
Amount Of Data Grows Rapidly

As of June 2003, there were 32528249295bases

in 25592865sequence

how to access them
How to access them

Main Sites

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

EMBL : http://www.embl-heidelberg.de/

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

  • full release every two months
  • incremental and cumulative updates daily
  • available only through internetftp://ftp.ncbi.nih.gov/genbank/
  • 66.3 Gigabytes of data
slide18

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

NCBI, a division of NLM at the NIH campus, USA

EXPASY : http://www.expasy.orgSwiss Institute of Bioinformatics

Kyoto Encyclopedia of Genes and Genomes

http://www.genome.ad.jp/kegg/kegg2.html

slide19

National Centre for Biotechnology Information

Established in 1988 as a national resource for molecular biology information, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information all for the better understanding of molecular processes affecting human health and disease.http://www.ncbi.nlm.nih.gov/

entrez

Entrez

Entrez is a search and retrieval system that integrates information from databases at NCBI.

slide25

Brief description of the sequence.

Accession Number : Unique identifier

Source : Organism’s common name

Formal scientific name

Contains information on the publications such as the authors, and topic titles of the journals that discuss the data reported in the record.

Contains the contact information of the submitter

  • Contains the information about the genes, gene products and regions of biological significance reported in the sequence &
  • length of sequence
  • scientific name of the source organism
  • Taxon ID number, Map location
slide26

Coding sequence (region of the nucleotides that correspond to the sequence of amino acid). This is also the location that contains the start and stop codon.

Region of biological interest

The amino acid translation corresponding to the nucleotide coding sequence

how to understand the output
How to understand the output

Unique Identifiers :

Each entry in a database must have a unique identifier

EMBL Identifier (ID)

GENBANK Accession Number (AC)

Other information is stored along with the sequence.

Each piece of information is written on it\'s own line, with a code defining the line. For example,

DE, description;

OS, organism species;

AC, accession number. Relevant biological information is usually described in the feature table (FT).

genbank flat file format
Genbank Flat File Format

Refer to Summary Description of the Genbank Flat File Format

Or

http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html

expasy
ExPASy
  • Expert Protein Analysis System proteomics server of the Swiss Institute of Bioinformatics (SIB)
  • dedicated to the analysis of protein sequences and structures http://www.expasy.org/
databases on the expasy server
Databases on the Expasy server
  • SWISS-PROT and TrEMBL - Protein knowledgebase
  • PROSITE - Protein families and domains
  • SWISS-2DPAGE - Two-dimensional polyacrylamide gel electrophoresis
  • ENZYME - Enzyme nomenclature
  • SWISS-3DIMAGE - 3D images of proteins and other biological macromolecules
  • SWISS-MODEL Repository - Automatically generated protein models
swiss prot
SWISS-PROT

A curated protein sequence database which strives to provide a high level of annotations (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databaseshttp://tw.expasy.org/sprot/

trembl
TrEMBL
  • Computer-annotated supplement to SWISS-PROT
enzyme

ENZYME

Enzyme nomenclature database

http://tw.expasy.org/enzyme/

enzyme database
ENZYME Database
  • A repository of information relative to the nomenclature of enzymes
  • Describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided
access to enzyme
Access to ENZYME
  • by EC number
  • by enzyme class
  • by description (official name) or alternative name(s)
  • by chemical compound
  • by cofactor
k e g g

K E G G

Kyoto Encyclopedia of Genes and Genomes

http://www.genome.ad.jp/kegg/kegg2.html

slide40
KEGG
  • Part of the GenomeNet database system
  • Linked to all accessible databases by search engines; LIGAND & BRITE
summary
Summary
  • Biological databases represent an invaluable resource in support of biological research.
  • We can learn much about a particular molecule by searching databases and using available analysis tools.
  • A large number of databases are available for that task. Some databases are very general while some are very specialised. For best results we often need to access multiple databases.
slide46
Common database search methods include keyword matching, sequence similarity, motif searching, and class searching
  • The problems with using biological databases include incomplete information, data spread over multiple databases, redundant information, various errors, sometimes incorrect links, and constant change.
slide47
Database standards, nomenclature, and naming conventions are not clearly defined for many aspects of biological information. This makes information extraction more difficult
  • Retrieval systems help extract rich information from multiple databases. Examples include Entrez and SRS.
  • Formulating queries is a serious issue in biological databases. Often the quality of results depends on the quality of the queries.
  • Access to biological databases is so important that today virtually every molecular biological project starts and ends with querying biological databases.
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