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Biobank for Translational Medicine: Standard Operating Procedures for Optimal Sample Management

Biobank for Translational Medicine: Standard Operating Procedures for Optimal Sample Management

Published on: November 30, 2022

GenBank.

Dennis A Benson¹, Ilene Karsch-Mizrachi, David J Lipman

¹National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.

Nucleic Acids Research

|November 14, 2009

Summary

This summary is machine-generated.

GenBank is a comprehensive nucleotide sequence database, housing data from over 300,000 organisms. It ensures worldwide coverage through daily data exchange and provides access via the NCBI Entrez system.

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Area of Science:

Bioinformatics
Genomics
Molecular Biology

Background:

GenBank is a critical repository for publicly available nucleotide sequences.
It encompasses data from over 300,000 organisms, sourced from individual labs and large-scale projects.
Data is primarily obtained through whole genome shotgun and environmental sampling initiatives.

Purpose of the Study:

To describe the scope and accessibility of the GenBank database.
To highlight the data submission and accessioning processes.
To outline the integration of GenBank with other NCBI resources for comprehensive data retrieval and analysis.

Main Methods:

Data collection through laboratory and large-scale sequencing project submissions (e.g., WGS, environmental sampling).
Utilizing web-based (BankIt) and standalone (Sequin) programs for data submission.
Ensuring worldwide coverage via daily data exchange with ENA and DDBJ.

Main Results:

GenBank contains nucleotide sequences from over 300,000 organisms.
Accession numbers are assigned by GenBank staff upon submission.
Data is accessible through the NCBI Entrez system, integrating diverse biological information.

Conclusions:

GenBank is a vital, globally-connected resource for nucleotide sequence data.
It facilitates research through integrated access with other NCBI databases and tools like BLAST.
Regular updates and FTP access ensure the database remains current and readily available.