DinoREF: Dinoflagellate 18S rRNA Gene Reference Database

DinoREF is a curated reference database for the 18S rRNA gene of dinoflagellates (Dinophyceae). The database includes sequences from GenBank and literature sources, annotated with multiple taxonomy classifications and clustered into OTUs. Solenn Mordret and colleagues submitted the associated paper for revision in 2018.

Use Cases

• Taxonomic classification of dinoflagellate sequences based on the provided 8-level and superclade taxonomy files.
• Clustering and operational taxonomic unit (OTU) analysis based on the provided 98% OTU and unique V4 region lists.
• Reference-based sequence alignment and phylogenetic analysis using the provided FASTA files of 18S and early-branching dinoflagellate sequences.

Strengths

• The database is curated, suggesting manual verification of entries from GenBank and literature sources.
• Provides multiple taxonomy classifications (GenBank, 8-level, superclades) for each sequence.
• Includes pre-clustered OTUs at 98% similarity and lists of unique V4 region sequences to aid analysis.

Limitations

• Row count and total size of the database are unknown, which may limit suitability assessment.
• Column-level documentation is absent; field semantics must be inferred from supplementary material descriptions after download.
• Last update date is unknown; freshness unverified as the associated paper was under revision in 2018.

Provenance

Source

GenBank and literature sources, as curated by the authors.

Collection Method

Curated compilation and annotation of publicly available 18S rRNA gene sequences.