Echinobase

Echinobase provides a multispecies genomic knowledgebase for echinoderms that integrates gene pages, genome assemblies, JBrowse, BLAST+, an echinoderm anatomical ontology, formal gene nomenclature, and orthology predictions to support genomics, developmental biology, and gene regulatory network analyses.

Key Features:

• Supported species: Contains data for six echinoderm species relevant to genomics, developmental biology, and gene regulatory network studies.
• Gene pages: Hosts over 38,000 detailed gene pages describing echinoderm genes.
• Publications: Indexes access to more than 18,000 publications relevant to echinoderm research.
• Genome assemblies: Provides improved genome assemblies for supported echinoderm species.
• JBrowse integration: Includes the JBrowse genome browser for genome visualization and exploration.
• BLAST+ services: Offers BLAST+ services for sequence similarity searches against echinoderm genomic data.
• Multispecies integration: Supports integration and analysis of multiple, disparate echinoderm genomes and the addition of new genomes as they become available.
• Echinoderm anatomical ontology: Implements a novel echinoderm anatomical ontology for consistent anatomical annotation.
• Formal gene nomenclature: Applies uniformly formatted gene nomenclature across species.
• Orthology predictions: Provides consistent orthology predictions for comparative analyses.
• Shared software stack and infrastructure: Built on a shared software stack and infrastructure including private cloud services and physical hosts originally developed for Xenbase.

Scientific Applications:

• Comparative genomics: Enables comparative genomic analyses across multiple echinoderm species using genome assemblies, orthology data, and JBrowse.
• Developmental biology: Supports developmental biology research through anatomical ontology-linked gene annotations and literature integration.
• Gene regulatory network analysis: Facilitates gene regulatory network studies by providing curated gene pages, genome context, and publication references.
• Sequence similarity searches: Enables sequence-based identification and comparison using BLAST+ against echinoderm datasets.

Methodology:

The platform was constructed by cloning and refactoring the Xenbase knowledgebase to support multispecies content, built on a shared software stack and infrastructure including private cloud services and physical hosts, and integrates JBrowse and BLAST+ while incorporating a novel echinoderm anatomical ontology, uniformly applied gene nomenclature, and consistent orthology predictions.