Biological database | nucleic acid and protein sequence database | primary and secondary database

Introduction As biology has increasingly turned into a data-rich science, the need for storing and communicating large datasets has grown tremendously. The obvious examples are the nucleotide sequences, the protein sequences, and the 3D structural data produced by X-ray crystallography and macromolecular NMR. A new field of science dealing with issues, challenges and new possibilities created by these databases has emerged: bioinformatics. Bioinformatics is the application of Information technology to store, organize and analyze the vast amount of biological data which is available in the form of sequences and structures of proteins (the building blocks of organisms) and nucleic acids (the information carrier). The biological information of nucleic acids is available as sequences while the data of proteins is available as sequences and structures. Sequences are represented in single dimension where as the structure contains the three dimensional data of sequences. Sequences and structures are only among the several different types of data required in the practice of the modern molecular biology. Other important data types includes metabolic pathways and molecular interactions, mutations and polymorphism in molecular sequences and structures as well as organelle structures and tissue types, genetic maps, physiochemical data, gene expression profiles, two dimensional DNA chip images of mRNA expression, two dimensional gel electrophoresis images of protein expression, data A biological database is a collection of data that is organized so that its contents can easily be accessed, managed, and updated. There are two main functions of biological databases: • Make biological data available to scientists. o As much as possible of a particular type of information should be available in one single place (book, site, and database). Published data may be difficult to find or access and collecting it from the literature is very time- consuming. And not all data is actually published explicitly in an article (genome sequences!). • To make biological data available in computer-readable form. o Since analysis of biological data almost always involves computers, having the data in computer-readable form (rather than printed on paper) is a necessary first step. a Primary Nucleotide Sequence Repository – GenBank, EMBL, DDBJ These are three chief databases that store and make available raw nucleic acid sequences. GenBank is physically located in the USA and is accessible through NCBI portal over internet. EMBL (European Molecular Biology Laboratory) is in UK and DDJB (DNA databank of Japan) is in Japan. They have uniform data formats (but not identical) and exchange data on daily basis. Here we will describe one of the database formats, GenBank, in detail. The access to GenBank, as to all databases at NCBI is through the Entrez search program. This front end search interface allows a great variety of search options. .necessary first step. Primary Protein Sequence Repositories PIR-PSD or protein information resource – protein sequence database, at the NBRF (National Biomedical Research Foundation, USA), and SWISS-PROT at the SBI (Swiss Biotechnology Institute), Switzerland are protein sequence databases. The PIR-PSD is a collaborative endeavour between the PIR, the MIPS (Munich Information Centre for Protein Sequences, Germany) and the JIPID (Japan International Protein Information Database, Japan). The PIR-PSD is now a comprehensive, non- redundant, expertly annotated, object relational DBMS. It is available at pir.georgetown.edu/pirww. A unique characteristic of the PIR-PSD is its classification of protein sequences based on the super family concept. Sequence in PIR- PSD is also classified based on homology domain and sequence motifs. Homology domains may correspond to evolutionary building blocks, while sequence motifs represent functional sites or conserved regions. The classification approach allows a more complete understanding of sequence function structure relationship. relationship ....more - www.nsscnilamel.org/images/Download/4198570bed66b6… #database

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