Notice for users using old version of Web browsers

We detect your browser version and show this notice for you.
This website has been developed by HTML5 web standard, so that old versions of web browsers have several problems for showing web pages. Of course, we are endeavoring to support such web browsers which are not support HTML5 totally.
However, it might be slightly difficult for you to use all of functions in this site normally because of some of lacks.
We strongly recommend you to update your browser. If your browser is Internet Explorer(IE) and it is unavailable to update to IE 10 in your computer, please use another up-to-date browsers.( FireFox, Chrome, Opera )
Your feedback is always welcome. Please send your comment to us.

About GRD

  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

Methodology

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

 

 

 

 

Back to Top