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GRD is a manually-curated 16S rRNA database, in which both the 5' and 3' regions, including the anti-SD sites, have been carefully checked and contaminating sequences have been removed. Current 16S rRNA gene sequences, including GenBank annotations, in existing 16S rRNA databases constructed from complete genomes often contain misannotations or are missing the anti-SD site and other short segments due to the erroneous removal of PCR primer regions. Hence, the need for a manually-curated 16S rNRA database for more reliable taxonomic classification.
Use GRD to:
- Search for Bacterial or Archaeal information and 16S sequences by taxonomic name or various keywords from the main search page
- Gather each information and sequences from the Phylogenetic Tree page
- Perform similarity search with this database using your own 16S complete or partial sequences in SeqSearch page
- Download all or specified 16S sequences to use for other analyses
Structure of 16S rRNA gene and minimum acceptable region for inclusion in GRD
Detection of 16S rRNA genes from publicly available genomes
We downloaded 2,275 complete and 5,664 draft genome sequences including the Human Microbiome Project (HMP) genome sequences data from NCBI (2013. Feb), and performed similarity analysis with the 16S rRNA gene sequence annotated in Escherichia coli str. K-12 substr. W3110 as our reference sequence using GLSEARCH (version 36.3.5e). We extracted 16S rRNA candidate sequences with global/local scores ≥ 0 with the E. coli 16S rRNA gene sequence.
Curation of 16S rRNA candidate sequences from complete genome sequences
Curation of 16S rRNA candidate sequences from draft genome sequences