Nucleic Acid databases

 Nucleotide Sequence Databases

 Nucleotide Sequence Databases are data repositories that accept nucleic acid sequence data and make it freely available to public. The data in these repositories are heterogenous with respect to the source of material, quality, annotation and intended completeness of sequence relative to its biological target.

 Nucleotide Sequence Databases are of 2 types

1) Primary Sequence Databases- Genbank, EMBL, DDBJ, TrEMBL 

2) Secondary Sequence Databases-Swiss Prot, Prosite, PDB

International  Nucleotide Sequence Database Collaboration consist mainly 3 databases; Genbank, EMBL, DDBJ. These 3 databases exchange and update data on a daily basis to achieve optimal synchronization.

Genbank

GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences .It is a primary database of nucleotide. GenBank is accessed and searched through Entrez gateway at NCBI. User can download entire database as flat files. GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA Data Bank of Japan (DDBJ), the European Nucleotide Archive (ENA), and GenBank at NCBI. These three organizations exchange data on a daily basis. A GenBank release occurs every two months and is available from the ftp site. The release notes for the current version of GenBank provide detailed information about the release and notifications of upcoming changes to GenBank. Release notes for previous GenBank releases are also available. Here information starts with the line containing the word “LOCUS”. Each  entry in 

EMBL

The European Molecular Biology Laboratory (EMBL) is a nucleotide sequence database maintained at the European Bioinformatics Institute (EBI) in an international collaboration with the DNA Data Bank of Japan (DDBJ) and GenBank (USA). Data is exchanged amongst the collaborative databases on a daily basis. The major contributors to the EMBL database are individual authors and genome project groups. EMBL is a primary nucleotide sequence database in Europe. Network services allow free access to the most up-to-date data collection via Internet and WWW interfaces. EBI's Sequence Retrieval System (SRS) is a network browser for databanks in molecular biology, integrating and linking the main nucleotide and protein databases plus many specialised databases. For sequence similarity searching a variety of tools (e.g., BLITZ, FASTA, BLAST) are available which allow external users to compare their own sequences against the most currently available data in the EMBL Nucleotide Sequence Database and SWISS-PROT.

DDBJ

DDBJ is a Primary nucleotide sequence database in Japan. The DNA Data Bank of Japan (DDBJ) is a biological database that collects DNA sequences. It is located at the National Institute of Genetics (NIG) in the Shizuoka prefecture of Japan. It is also a member of the International Nucleotide Sequence Database Collaboration or INSDC. It exchanges its data with European Molecular Biology Laboratory at the European Bioinformatics Institute and with GenBank at the National Center for Biotechnology Information on a daily basis.  Presently, sequence submission to either GenBank, EMBL, or DDBJ is a precondition for publication in most scientific journals to ensure the fundamental molecular data to be made freely available.

Secondary Sequence Databases

Unigene

STACK

Ribosomal Database project

HIV Sequence database

Eukaryotic promoter database

REBASE

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