23S rDNA Plastidial Reference database

Downloads

µgreen-db r1.1 2019-09-06 Last release (Zenodo repository)
  1. All reference database (2,326 plastidial 23S rRNA sequences with 1,388 Eukaryota and 938 Bacteria) at fasta format.
  2. Full length sequences and AlgaeBase taxonomy reference (2,326 plastidial 23S rRNA sequences with 1,388 Eukaryota and 938 Bacteria):
    • BIOCOM-PIPE format (FASTA with Taxonomy)
    • mothur format
    • Taxonomy file only
  3. Full length sequences and NCBI taxonomy reference (2,326 plastidial 23S rRNA sequences with 1,388 Eukaryota and 938 Bacteria):
    • BIOCOM-PIPE format
    • mothur format
    • Taxonomy file only
  4. Full length sequences and PR2/SILVA taxonomy reference (2,217 plastidial 23S rRNA sequences with 1,341 Eukaryota and 876 Bacteria):
    • BIOCOM-PIPE format
    • mothur format
    • Taxonomy file only

Taxonomy file description

The taxonomy file: It is a 2 column file with the following format: sequenceID tab taxonomy lineage specific to each nomenclature (NCBI, AlgaeBase, PR2/SILVA).

Fasta file description

Full length sequences: the associated identifier is in the following form: [C or I or E]AccessionNumber.Letter(if duplicate).start.end;AllLineage where ‘C’ signifies complete, ‘I’ incomplete and ‘E’ environmental.

BIOCOM-PIPE file description

BIOCOM-PIPE format:
Example:

Eukaryota(domain);Stramenopiles(supergroup);Ochrophyta(phylum);Eustigmatophyceae(class);Eustigmatophyceae_X(order);Eustigmatophyceae_XX(family);Nannochloropsis(genus);Nannochloropsis_oculata

mothur file description

Mothur format:
Example:

d__Eukaryota;p__Ochrophyta;c__Eustigmatophyceae;o__Eustigmatophyceae_X;f__Eustigmatophyceae_XX;g__Nannochloropsis;s__Nannochloropsis_oculata;