EchinoDB

EchinoDB provides integrated access to echinoderm genomic and transcriptomic datasets, organizing orthologous and paralogous transcripts into orthoclusters to support comparative and evolutionary analyses.

Key Features:

• Extensive Data Collection: Contains 749,397 transcripts from diverse echinoderm species, with orthologous and paralogous transcripts organized into orthoclusters based on sequence similarity.
• Species-specific Datasets: Includes RNA-seq data from the brittle star Ophioderma brevispinum and a high-quality genomic assembly from the green sea urchin Lytechinus variegatus.
• Search and Similarity Tools: Supports keyword searches of annotated records and similarity searches using BLAST via an updated Sequenceserver.
• Data Format and Download: Provides sequence data available for download in FASTA format.

Scientific Applications:

• Phylogenetics: Enables reconstruction of evolutionary relationships across echinoderm classes using orthologous and paralogous transcript data.
• Developmental Biology: Supports analysis of gene regulatory networks and developmental pathways in echinoderms.
• Regeneration Studies: Facilitates identification of genes and pathways involved in tissue regeneration in echinoderms.
• Comparative Genomics: Enables comparative genomic analyses across species to study genetic diversity and evolutionary adaptations.
• Physiology and Neurobiology: Provides sequence resources for investigations into echinoderm physiology and neurobiology.

Methodology:

Organizes orthologous and paralogous transcripts into orthoclusters based on sequence similarity, provides BLAST searches via Sequenceserver, and distributes RNA-seq and genomic assembly datasets in FASTA format.