Bioinformatics Bioinformatics Databases

International Nucleotide Sequence Database Collaboration

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The International Nucleotide Sequence Database Collaboration (INSDC) is a long-standing foundational initiative that operates between DDBJ, EMBL-EBI and NCBI. INSDC covers the spectrum of data raw reads, through alignments and assemblies to functional annotation, enriched with contextual information relating to samples and experimental configurations. The INSDC advisory board, the International Advisory Committee, is made up of members of each of the databases’ advisory bodies. 

The DDBJ/EMBL/GenBank synchronization is maintained according to a number of guidelines which are produced and published by an International Advisory Board. 

Its syntax is called INSDSeq and its core consists of the letter sequence of the gene expression and the letter sequence for nucleotide bases in the gene or decoded segment. 

The Taxonomy Project

One of the goals of the collaborators is to use a unified taxonomy across all databases, largely one based on sequence information. The taxonomy project was set up as a tool for biologists worldwide, and also as a shared instrument for the collaborators. This is one of the important resources used for the maintenance of Genetic Codes, important for the correct translation of coding sequences.

The Feature Table

The Feature Table documentation shows the shared rules that allow the three databases to exchange data on a daily basis. The Feature Table shows the vocabulary that is used to describe the DNA sequence annotations as well as that of the protein sequence(s) they encode.

Under the International Nucleotide Sequence Database Collaboration globally comprehensive public domain nucleotide sequence is captured, preserved and presented. The partners of this long-standing collaboration work closely together to provide data formats and conventions that enable consistent data submission to their databases and support regular data exchange around the globe. Clearly defined policy and governance in relation to free access to data and relationships with journal publishers have positioned INSDC databases as a key provider of the scientific record and a core foundation for the global bioinformatics data infrastructure. While growth in sequence data volumes comes no longer as a surprise to INSDC partners, the uptake of next-generation sequencing technology by mainstream science that we have witnessed in recent years brings a step-change to growth, necessarily making a clear mark on INSDC strategy.

The DNA Data Bank of Japan (DDBJ)

Search for comprehensive information on genes, proteins, and genomes.

European Bioinformatics Institute web services (EBI)

It finds and uses various bioinformatics tools from this huge collection at EBI.

GenBank

Search for nucleotide sequences from 300000+ named organisms.

National BioResource Project (NBRP)

Access database resources available through the NBRP.

The National Center for Biotechnology Information (NCBI)

Search a huge collection of molecular biology and bioinformatics databases.

The EMBL Nucleotide Sequence Database

Search comprehensive collection of nucleotide sequences and annotation from available public sources.

The European Bioinformatics Institute’s data resources

Search and use an extensive collection of molecular biology databases and tools.

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