dbfetch

dbfetch retrieves biological records from EMBL-EBI databases using entry identifiers or accession numbers to support sequence retrieval, integration with EBI Search, and downstream sequence analysis via the Job Dispatcher framework.

Key Features:

• Integrated Access: Provides integrated access to EMBL-EBI-managed biological databases for retrieval of sequences and associated metadata.
• Identifier-based Retrieval: Retrieves entries using entry identifiers and accession numbers across EMBL-EBI resources.
• Full-Text Search Capability: Leverages the EBI Search interface (https://www.ebi.ac.uk/ebisearch) to perform full-text queries across nearly 5 billion entries.
• Sequence Analysis Integration: Integrates with the Job Dispatcher tools framework (https://www.ebi.ac.uk/services) to enable use of bioinformatics applications for sequence analysis.
• API Support: Exposes RESTful and SOAP-based APIs for programmatic access, automation, and integration with external workflows.

Scientific Applications:

• Genomics: Retrieval of genomic sequences and metadata for comparative genomics and variant analysis.
• Proteomics: Access to protein sequences and annotations to support proteomics workflows.
• Transcriptomics: Provision of transcript and sequence data for transcriptomic analyses and annotation.
• Pandemic pathogen genomics: Rapid access to up-to-date SARS-CoV-2 and other pathogen sequences to support surveillance and outbreak analysis.

Methodology:

Leverages EMBL-EBI data resources together with EBI Search full-text search and the Job Dispatcher tools framework, and exposes RESTful and SOAP APIs to retrieve records by entry identifiers or accession numbers.