Home / Release archive / 7.213

Contents

• Downloads
  • RiboGrove release 7.213
  • 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
• Searching data in RiboGrove
  • Header format
  • Search sequences by header
  • Search sequences by length
  • Selecting header data

Downloads

RiboGrove release 7.213 (2022-07-20)

The release is based on RefSeq release 213.

• A fasta file of full-length 16S gene sequences. Download (gzipped fasta file, 5.87 MB)
• A “raw“ version of the fasta file above. This file contains partial sequences. Download (gzipped fasta file, 6.16 MB)
• Metadata Download (zip archive 19.89 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).
  9. QIIME2-compatible-taxonomy.txt
     This is a TSV file, which can be used to train a QIIME2 classifier (see the tutorial).

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%.

Searching data in RiboGrove

RiboGrove is a very minimalistic database — it comprises a collection of plain fasta files with metadata. Thus, extended search instruments are not available for it. We admit this problem and provide a list of suggestions below. The suggestions would help you to explore and select RiboGrove data.

Header format

RiboGrove fasta data has the following format of header:

>NZ_CP079719.1:86193-87742_plus Bacillus_velezensis ;Bacteria;Firmicutes;Bacilli;Bacillales;Bacillaceae;Bacillus; category:2

Major blocks of a header are separated by spaces. A header consists of four such blocks:

1. Sequence ID (seqID): NZ_CP079719.1:86193-87742_plus. SeqID, in turn, consists of three parts:
   1. the accession number of the RefSeq sequence, from which the gene originates: NZ_CP079719.1;
   2. coordinates of the gene within this RefSeq genomic sequence: 86193-87742 (coordinates are 1-based, left-closed and right-closed);
   3. strand of the RefSeq genomic sequence, where the gene is located: plus (or minus).
2. The complete name of the organism, according to the NCBI Taxonomy database: Bacillus_velezensis.
3. Taxonomy string, comprising domain (Bacteria), phylum (Firmicutes), class (Bacilli), order (Bacillales), family (Bacillaceae), and genus (Bacillus) names. The names are separated and flanked by semicolons (;).
4. The category of the genome, from which the gene sequence originates: (category:2). Category 1 genomes are of the highest reliability, and category 3 genomes are least reliable.

Sequence selection

You can select specific sequences from fasta files using the Seqkit program (GitHub repo, documentation). It is free, cross-platform, multifunctional and pretty fast and can process both gzipped and uncompressed fasta files. Programs seqkit grep and seqkit seq are useful for sequence selection.

Search sequences by header

Given the downloaded fasta file ribogrove_7.213_sequences.fasta.gz, consider the following examples of sequence selection using seqkit grep:

Example 1. Select a single sequence by SeqID.

seqkit grep -p "NZ_CP079719.1:86193-87742_plus" ribogrove_7.213_sequences.fasta.gz

The -p option sets a pattern to search in fasta headers (only in sequence IDs, actually).

Example 2. Select all gene sequences of a single RefSeq genomic sequence by accession number.

seqkit grep -nrp "NZ_CP079719.1" ribogrove_7.213_sequences.fasta.gz

Here, two more options are required: -n and -r. The former tells the program to match the whole headers instead of IDs only. The latter tells the program not to exclude partial matches from output, i.e. if the pattern is a substring of a header, the header will be printed to output.

Example 3. Select all gene sequences of a single genome (Assembly ID 10577151), which has two replicons: NZ_CP079110.1 and NZ_CP079111.1.

seqkit grep -nr -p "NZ_CP079110.1" -p "NZ_CP079111.1" ribogrove_7.213_sequences.fasta.gz

Example 4. Select all actinobacterial sequences.

seqkit grep -nrp ";Actinobacteria;" ribogrove_7.213_sequences.fasta.gz

Just in case, surround the taxonomy name with semicolons (;).

Example 5. Select all sequences originating from category 1 genomes.

seqkit grep -nrp "category:1" ribogrove_7.213_sequences.fasta.gz

Example 6. Select all sequences except for those belonging to Firmicutes.

seqkit grep -nvrp ";Firmicutes;" ribogrove_7.213_sequences.fasta.gz

Recognize the -v option within the option sequence -nvrp. This option inverts match, i.e. without it the search would result in sequences belonging to Firmicutes only.

Search sequences by length

You can use the seqkit seq program to select sequences by length.

Example 1. Select all sequences longer than 1600 bp.

seqkit seq -m 1601 ribogrove_7.213_sequences.fasta.gz

The -m option sets the minimum length of a sequence to be printed to output.

Example 2. Select all sequences shorter than 1500 bp.

seqkit seq -M 1499 ribogrove_7.213_sequences.fasta.gz

The -M option sets the maximum length of a sequence to be printed to output.

Example 3. Select all sequences having length in range [1500, 1600] bp.

seqkit seq -m 1500 -M 1600 ribogrove_7.213_sequences.fasta.gz

Selecting header data

It is sometimes useful to retrieve only header information from a fasta file. You can use the seqkit seq program for it.

Example 1. Select all headers.

seqkit seq -n ribogrove_7.213_sequences.fasta.gz

The -n option tells the program to output only headers.

Example 2. Select all SeqIDs (header parts before the first space).

seqkit seq -ni ribogrove_7.213_sequences.fasta.gz

The -i option tells the program to output only sequence IDs.

Example 3. Select all accession numbers.

seqkit seq -ni ribogrove_7.213_sequences.fasta.gz | cut -f1 -d':' | sort | uniq

This might be done only if you have sort, cut and uniq utilities installed (Linux and Mac OS systems should have them built-in).

RiboGrove, 2023-05-19