Bioinformatics

Biological Databases

1. Why Databases ? I 2. Database classification I 3. Additional information

2. Database classification

In recent years, biological databases have greatly developed and increased very well, and they became a normal part of the biologist's everyday toolbox.
Biological databases can be broadly classified into sequence and structure databases. In general, databases can be furthermore classified into primary, secondary and composite databases.

primary databases(consisting of data derived experimentally)

• grown tremendously over the years
• contains information of the sequence or structure alone and associated annotation information

a.) sequence databases

 

DNA / nucleotide databases
	EMBL	Nucleotide Sequence Database main sources for DNA and RNA sequences direct submissions form individual researchers, genome sequencing projects and patent applications	produced in an international collaboration with GenBank (USA) and the DNA Database of Japan (DDBJ)
		EnsEMBL presents up-to-date sequence data and the best possible annotation for metazoan genomes	joint project between EMBL and the Sanger Institute
	GenBank	Genetic Sequence Database annotated collection of all publicly available DNA sequences	part of the International Nucleotide Sequence Database Collaboration consists of the DNA Data Bank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank (NCBI) data exchange data on a daily basis
	DDBJ	DNA Data Bank of Japan	established in 1986 at the National Institute of Genetics (NIG) reorganized as the Center for Information Biology and DNA Data Bank of Japan (CIB/DDBJ) in 2001
Protein databases
	Swiss-Prot	annotated protein sequence database high level of annotation (thoroughly analyzed and annotated by biologists) and integration with other biomolecular databases + documentation minimal level of redundancy	established in 1986 maintained collaboratively by the EMBL Outstation (EBI) and the Swiss Institute of Bioinformatics (SIB)
	TrEMBL	Translation of EMBL Nucleotide Sequence Databases make new sequences available as quickly as possible computer-annotated entries derived from the translation of all coding sequences (CDS) in EMBL	created in 1996 supplement to Swiss-Prot
	PIR	Protein Information Resource partitioned into four sections by differences in classification, annotation and redundancy cross-referencing to other biological databases	established in 1984 by the National Biomedical Research Foundation (NBRF) since 1988 maintained by PIR-International
		PSD	Protein Sequence Database

b.) structure databases

 

	PDB	Protein Data Bank single worldwide repository for processing and distribution of 3-D biological macromolecular structure data
	NDB	Nucleic Acid Database repository of 3-D structural information about nucleic acids
	CCDB / CSD	Cambridge Crystallographic Data Centre / Cambridge Structural Database compilation of a computerised database containing comprehensive data for organic and metal-organic compounds studied by X-ray and neutron diffraction

• contains derived information from a primary database, like information about conserved sequence, signature sequence and active site residues of the protein families arrived by multiple sequence alignment of a set of related proteins
• secondary structure database contains entries of the PDB in an organized way (for instance, by classification of all PDB entries according to structures like alpha-helix or ß-sheets) and also information on conserved secondary structure motifs of a particular protein

 

Sequence-related Information
	ProSite	Database of Protein Families and Domains contains patterns and profiles specific for more than a thousand protein families or domains + background information on the structure and function of these proteins
	Pfam	Protein Families Database of Alignment and HMMs large collection of multiple sequence alignments and hidden Markov models covering many protein domains and families
	Enzyme	Enzyme Nomenclature Database repository of information relative to the nomenclature of enzymes	primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB)
	REBase	Restriction Enzyme Database collection of information about restriction enzymes and related proteins
Genome-related Information
	OMIM	Online Mendelian Inheritance in Man catalog of human genes and genetic disorders includes information on genetic variation in humans contains textual information, pictures, and reference information	incorporated into NCBI's Entrez system and can be queried using the same approach as the other Entrez databases such as PubMed and GenBank
	TransFac	Transcription Factor Database database on eukaryotic cis-acting regulatory DNA elements and trans-acting factors covers the whole range from yeast to human
Structure-related Information
	DSSP	Database of Secondary Structure Assignments secondary structure assignments for all protein entries in the Protein Data Bank (PDB)	designed by Wolfgang Kabsch and Chris Sander
	HSSP	Homology-derived Secondary Structure of Proteins	designed by Chris Sander and Reinhard Schneider
	Dali	based on exhaustive all-against-all 3D structure comparison of protein structures currently in the Protein Data Bank (PDB)	classification and structure alignments are continuously updated
Pathway Information
	KEGG	Kyoto Encyclopedia of Genes and Genomes bioinformatics resource for understanding higher order functional meanings and utilities of the cell or the organism from its genome information	suite of databases and associated software, integrating knowledge on molecular interaction networks in biological processes, the information about the universe of genes and proteins, and the information about the universe of chemical compounds and reactions

• joins a variety of different primary database sources, which obviates the need to search multiple resources

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