seqxref

seqxref retrieves all database cross-references associated with a given sequence entry to support integration of sequence annotations within the EMBOSS framework.

Key Features:

• Integration with EMBOSS: Integrates with the EMBOSS suite and interoperates with over 200 EMBOSS applications.
• Database configuration and querying: Supports configuration and querying of databases under EMBOSS to retrieve sequence cross-references.
• Extensibility via C libraries and ACD files: Leverages EMBOSS C programming libraries and Application Configuration Descriptor (ACD) files to enable development and customization.
• Third-party tool wrapping: Supports wrapping and porting of third-party bioinformatics tools into the EMBOSS environment for inclusion in cross-referencing workflows.

Scientific Applications:

• Gene annotation: Provides cross-references that assist in gene annotation by linking sequence entries to related database records.
• Comparative genomics: Facilitates identification and linking of homologous sequences across databases for comparative genomics analyses.
• Functional analysis: Enriches sequence datasets with cross-referenced functional information to support functional analysis.
• Dataset validation and enrichment: Aggregates related database entries to support validation and enrichment of biological datasets.

Methodology:

Operates within the EMBOSS environment, configures and queries EMBOSS-managed databases to retrieve cross-references, and uses EMBOSS C programming libraries and ACD files for extensibility.