GenBank

Shivi Forensics

Topic: GenBank
Created By:
Sejal Odedara
Volunteer 
Shivi Forensics 

Introduction 
GenBank is comprehensive public database of nucleotide sequence and supporting bibliographic and biological annotation. The GenBank (Registered Trademark symbol) sequence database incorporates DNA sequences from all available public sources, primarily through the direct submission of sequence data from individual laboratories and from large-scale sequencing projects. GenBank data is accessible through NCBI's integrated retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome and protein structure information.

History 
GenBank was created in 1979 at the Los Alamos National Laboratory and was called the Los Alamos Sequence Database. It was renamed GenBank in 1982. And became a public database.
During 1989 to1992, GenBank transitioned to the newly created NCBI, a division of the National Library of Medicine (NLM), located on the campus of the US NIH in Bethesda, MD.
GenBank is built and distributed by NCBI. NCBI began accepting direct submission of GenBank in 1993. Since its creation GenBank has grown at an exponential rate, doubling in size every 18 months.
Data exchange with the EMBL Data Library and the DNA Data Bank of Japan helps ensure comprehensive worldwide coverage.

WORKING & FUNCTION

Building The Database
The data in GenBank and he collaborating databases EMBL and DDBJ, come from two sources: (1) individual authors who submit data directly to one of the databases, and (2) bulk submission from sequencing centers in the form of ESTs, STSs, GSSs or large genomic records (usually sequences from cosmids, BACs or YACs). Data are exchanged daily with DDBJ and EMBL so that the daily updates from NCBI servers incorporate the most recently available sequence data from all sources.


RETRIEVING GenBank DATA

1. The Entrez system:
It is a integrated database retrieval system that accesses DNA and protein sequence data, genome mapping data, population sets, the NCBI taxonomy, protein structures from the Molecular Modeling Database, MMDB (11) and MEDLINE reference via PubMed.
2. BLAST sequence- similarity searching
The most frequent type analysis performed using GenBank search for sequences similar to a query sequence. NCBI offers the BLAST family of programs to locate good alignment between a query sequence and database sequence. Its searching is provided on NCBI’s web site.
3. Obtaining GenBank by FTP
NCBI used the ASN data format for internal maintenance of GenBank, but distributes the GenBank release (issued every 2 month) and the daily updates (which also incorporate sequence data from EMBL and DDBJ) are available by anonymous FTP from ‘ncbi.nlm.nih.gov’.


NLM GenBank and SRA data processing
The National Library of Medicine's (NLM's) National Center for Biotechnology Information (NCBI) manages the GenBank and Sequence Read Archive (SRA) databases of genetic sequence information.
1. How sequence data are submitted, processed, and made available to the 
2. Public responsibilities of the sequence data submitter and NCBI 
3. Key definitions of data status.



SUBMITING DATA:
At the time of submission, the submitter may specify a desired public release date for the sequence data (e.g., to align with the anticipated date of publication of a journal article). Submitters may request that private data be made publicly available prior to the scheduled release date or request that the release date be extended (e.g., to align with the anticipated date of publication of a journal article).

PROCESSING SUBMISSION:
NCBI processes submissions in the order received. However, NCBI may prioritize processing of submissions related to a pandemic or public health emergency. Upon the submitter's request, NCBI may also prioritize processing of submissions associated with an upcoming publication release.

PUBLICALY ACCESSIBLE:
Sequence data may become publicly available at different times across these NCBI storage locations, websites, APIs, and analysis tools as the newly released data propagates across the system. Upon release, publicly accessible sequence data are searchable by accession number in website interfaces. NCBI also indexes the data to support text-based searches (e.g., by organism name) in websites and APIs.

BLAST for nucleotide sequence:





REFERENCE:

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