Home / Release archive / 4.210

Contents

• Downloads
  • RiboGrove 4.210
  • RiboGrove release archive
• Statistical summary
  • RiboGrove size
  • 16S rRNA gene lengths
  • 16S rRNA gene copy number
  • Top-10 longest 16S rRNA genes
  • Top-10 shortest 16S rRNA genes
  • Top-10 genomes with the largest 16S rRNA copy numbers
  • Top-10 genomes with the highest intragenomic variability of 16S rRNA genes

Downloads

RiboGrove release 4.210 (2022-01-12)

The release is based on RefSeq release 210.

• A fasta file of full-length 16S gene sequences. Download (gzipped fasta file, 5.25 MB)
• A raw version of the fasta file above. This file contains partial sequences. Download (gzipped fasta file, 5.50 MB)
• Metadata Download (zip archive 15.50 MB)
  
  What information exactly does the metadata contain?

  The metadata consists of the following files:

  1. source_RefSeq_genomes.tsv
     This is a TSV files, which contains information about what genomes were used for the RiboGrove construction.
  2. gene_seqs_statistics.tsv, raw_gene_seqs_statistics.tsv
     These are TSV file, which contains nucleotide conposition, size, genomic and taxonomic affiliation of the gene sequences. The “raw” file also includes information about partial genes.
  3. per_replicon_statistics.tsv, raw_per_replicon_statistics.tsv
     These are TSV files, which contain information about number of 16S rRNA genes in each RefSeq genomic sequences, and about sizes of these genes. The “raw” file also includes information about partial genes.
  4. categories.tsv
     This is a TSV file, which contains information about what genome categories were assigned to each genome and why. Moreover, it contains information about what sequencing technology was used to sequence each genome.
  5. taxonomy.tsv
     This is a TSV file, which contains taxonomic affiliation of each genome and gene.
  6. intragenic_repeats.tsv
     This is a TSV file, which contains information about intragenomic repeats found in gene sequences using RepeatFinder.
  7. cmscan_output_table.tblout
     This is a TSV file, which contains complete output of cmscan program outputted after processing all 16S rRNA sequences.
  8. entropy_summary.tsv
     This is a TSV file, which contains summary of instragenomic variability of the 16S rRNA genes. Intragenomic variability are calculated only for the category 1 genomes having more than one 16S rRNA gene. Intragenomic variability is evaluated using Shannon entropy. We align gene sequences from each genome using MUSCLE, and then we calculate Shannon entropy for each multiple alignment column (i.e. base).

The fasta files are compressed with gzip, and the metadata file is a zip archive. To uncompress them, Linux and Mac OS users may use gzip and zip programs, they should be built-in. For Windows users, the free and open-source (de)compression program 7-Zip is available.

RiboGrove release archive

You can find all releases in the RiboGrove release archive.

Statistical summary

^* Metrics marked with this sign were calculated with preliminary normalization, i.e. median within-species gene length was used for the summary.

^* These are median within-species copy numbers.

^* Entropy is Shannon entropy calculated for each column of the multiple sequence alignment (MSA) of all full-length 16S rRNA genes of a genome. Entropy is then summed up (column "Sum of entropy") and averaged (column "Mean entropy").

^** Halomicrobium sp. ZPS1 is a quite remarkable case. This genome harbours two 16S rRNA genes, therefore entropy is equal to the number of mismatching nucleotides between sequences of the genes. Respectively, per cent of identity between these two gene sequences is 90.70%! This is remarkable because the usual (however arbitrary) genus demarcation threshold of per cent of identity is 95%.

RiboGrove, 2023-05-19