Entrez

Entrez provides integrated retrieval and cross-database linking of biological and biomedical data, including GenBank nucleotide sequences, protein sequences, taxonomic classifications, genome maps, protein structures, domain information, and related literature.

Key Features:

• Integrated database access: Aggregates data from GenBank, protein sequence records, taxonomy, genome mapping, protein structures, and domain annotations.
• GenBank content: Contains publicly available DNA sequences submitted by individual laboratories and large-scale sequencing projects from over 119,000 organisms.
• Submission and accessioning: Supports sequence submissions via BankIt and Sequin with accession numbers assigned upon receipt by GenBank staff.
• International data exchange: Maintains daily exchanges with the EMBL Data Library and the DNA Data Bank of Japan to ensure comprehensive global sequence coverage.
• Literature integration: Links NCBI database records with PubMed to connect sequence and annotation data to biomedical publications.
• Sequence similarity search: Enables sequence similarity searches using BLAST against GenBank and affiliated databases.
• Data releases and updates: Provides complete bimonthly GenBank releases and daily updates distributed via FTP.

Scientific Applications:

• Sequence similarity and comparative analysis: Use BLAST searches against GenBank for homology detection and comparative sequence studies.
• Genome annotation and mapping: Leverage nucleotide and genome map records for annotation and positional mapping tasks.
• Protein structure and domain analysis: Integrate protein sequence, structure, and domain information for structural and functional inference.
• Taxonomy and biodiversity studies: Employ taxonomic classifications and sequence records from >119,000 organisms for phylogenetics and biodiversity analyses.
• Literature-linked discovery: Combine sequence and annotation data with PubMed citations to support evidence-based interpretation and hypothesis generation.
• Data deposition and archival referencing: Submit and accession sequences for public archival, citation, and downstream reuse.

Methodology:

Entrez integrates database records with PubMed, supports BLAST sequence similarity searches, performs daily exchanges with EMBL and the DNA Data Bank of Japan, accepts submissions via BankIt and Sequin with accession numbers assigned by GenBank staff, and distributes bimonthly GenBank releases plus daily updates via FTP.