User Manual

1. Query all organisms based on taxonomy/word-based search:

The database can be searched based on taxonomy using a dropdown menu or directly through the search tab using keywords such as "Pseudomonadota", "Enterobacteriaceae", or by directly searching NCBI accession "GCA_000005845.2". For searching within particular taxonomic groups, users can select options like phylum, class, order, family, genus, and use the search box above them.

2. Search Results

2.1. Table with search results has:

• NCBI Assembly Accession: NCBI derived assembly ID of the genome with an external link directing to the NCBI genome assembly page of the particular organism.
• Taxonomy: Taxonomic classification containing the taxonomic lineage, including superkingdom, phylum, class, order, family, genus, and organism name.
• rRNA Count: Columns with 16S rRNA, 23S rRNA, and 5S rRNA copy numbers for the organism.

3. More Information on Each Organism's rRNAs

3.1. Page with detailed information includes:

• Organism Name: Derived from NCBI scientific name.
• NCBI TaxID and Taxonomy: Includes NCBI taxonomy ID with a link to the detailed NCBI taxonomy page.
• Genomic Features: Genome size, number of chromosomes and plasmids, GC percentage, and number of genes in the genome.
• Number of rRNA Copies: Copy numbers of 16S, 23S, and 5S rRNAs.
• Number of tRNA: Number of tRNAs present in the genome.
• Circos Plot: Circular representation of the genome with 16S (red), 23S (green), and 5S (black) highlighted.
• Sequence Viewer: Users can select replicons from a dropdown menu and search for locus tags of genes to visualize. A matrix beneath the page contains locus tags and accession details.
• Matrix: Homology-based percentage identity matrix of rRNA sequences using locus tags as identifiers and accessions for chromosomes/plasmids.
• Alignment of Sequences: Multiple sequence alignments of rRNA sequences.
• Secondary Structures: Secondary structures of rRNA sequences.

4. Statistics

This tab contains graphs describing the distribution of 16S, 23S, and 5S rRNA copies per phylum, along with other database statistics.