The main website where RiboGrove is hosted may be unavailable outside Belarus due to technical troubles and the overall disaster.
Hence this mirror has been created, and RiboGrove files are available through Dropbox (links are below).
Hence this mirror has been created, and RiboGrove files are available through Dropbox (links are below).
Home / Release archive / 1.207
Contents
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RiboGrove 1.207 (2021-12-08)
The release is based on RefSeq release 207.
- A fasta file of full-length 16S gene sequences. Download (gzipped fasta file, 4.81 MB)
- A
raw
version of the fasta file above. This file contains partial sequences. Download (gzipped fasta file, 5.04 MB) - Metadata Download (zip archive 13.54 MB)
What information exactly does the metadata contain?
The metadata consists of the following files:
-
source_RefSeq_genomes.tsv
This is a TSV files, which contains information about what genomes were used for the RiboGrove construction. -
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. -
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. -
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. -
taxonomy.tsv
This is a TSV file, which contains taxonomic affiliation of each genome and gene. -
intragenic_repeats.tsv
This is a TSV file, which contains information about intragenomic repeats found in gene sequences using RepeatFinder. -
cmscan_output_table.tblout
This is a TSV file, which contains complete output of cmscan program outputted after processing all 16S rRNA sequences. -
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).
-
source_RefSeq_genomes.tsv
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.
You may wonder, why RiboGrove 1.207 was released on December 8th, 2021, and RiboGrove 2.208 on November 25th, 2021. The reason is that initially (on October 28th, 2021), RiboGrove 1.207 wasn’t, strictly speaking, based on RefSeq 207 — it contained sequences, which had been added to RefSeq after release 207 but before release 208. The corrected version of RiboGrove 1.207 (2021-12-08) is based on RefSeq 207, without “contaminations” from RefSeq 208.
RiboGrove release archive
You can find all releases in the RiboGrove release archive.
Statistical summary
| Bacteria | Archaea | Total | |
|---|---|---|---|
| Number of gene sequences | 115,789 | 638 | 116,427 |
| Number of unique gene sequences | 33,668 | 444 | 34,112 |
| Number of species | 6,236 | 295 | 6,531 |
| Number of genomes | 22,333 | 381 | 22,714 |
| Number of genomes of category 1 | 14,357 | 88 | 14,445 |
| Number of genomes of category 2 | 7,852 | 293 | 8,145 |
| Number of genomes of category 3 | 124 | 0 | 124 |
| Bacteria | Archaea | |
|---|---|---|
| Minimum (bp) | 1,448.00 | 1,439.00 |
| 25th percentile (bp) * | 1,517.00 | 1,472.00 |
| Median (bp) * | 1,532.00 | 1,475.00 |
| 75th percentile (bp) * | 1,543.00 | 1,492.00 |
| Average (bp) * | 1,528.45 | 1,502.88 |
| Mode (bp) * | 1,537.00 | 1,471.00 |
| Maximum (bp) | 1,806.00 | 3,604.00 |
| Standard deviation (bp) * | 25.96 | 155.90 |
* Metrics marked with this sign were calculated with preliminary normalization, i.e. median within-species gene length was used for the summary.
| Copy number * | Number of species | Per cent of species (%) |
|---|---|---|
| 1 | 914 | 13.99 |
| 2 | 1,275 | 19.52 |
| 3 | 1,012 | 15.50 |
| 4 | 831 | 12.72 |
| 5 | 497 | 7.61 |
| 6 | 643 | 9.85 |
| 7 | 515 | 7.89 |
| 8 | 343 | 5.25 |
| 9 | 163 | 2.50 |
| 10 | 148 | 2.27 |
| 11 | 58 | 0.89 |
| 12 | 41 | 0.63 |
| 13 | 30 | 0.46 |
| 14 | 36 | 0.55 |
| 15 | 7 | 0.11 |
| 16 | 5 | 0.08 |
| 17 | 4 | 0.06 |
| 18 | 3 | 0.05 |
| 19 | 1 | 0.02 |
| 20 | 3 | 0.05 |
| 27 | 1 | 0.02 |
| 37 | 1 | 0.02 |
* These are median within-species copy numbers.
| Assembly ID | Gene length (bp) | RiboGrove Sequence ID (SeqID) | Organism |
|---|---|---|---|
| Bacteria | |||
| 8028891 | 1,806 | NZ_AP022826.1:1258017-1259822_minus NZ_AP022826.1:1532588-1534393_minus NZ_AP022826.1:1939914-1941719_minus |
Nitrosophilus labii |
| 282748 | 1,781 | NC_014964.1:2252888-2254668_minus | Thermoanaerobacter brockii |
| 40148 | 1,781 | NC_010321.1:2265744-2267524_minus | Thermoanaerobacter pseudethanolicus |
| 4499991 | 1,744 | NZ_CP043427.1:609141-610884_plus NZ_CP043427.1:930699-932442_minus NZ_CP043427.1:1503078-1504821_minus |
Campylobacter sputorum |
| 1153941 | 1,744 | NZ_CP019682.1:607981-609724_plus NZ_CP019682.1:929565-931308_minus NZ_CP019682.1:1501945-1503688_minus |
Campylobacter sputorum |
| 1153911 | 1,743 | NZ_CP019683.1:606847-608589_plus NZ_CP019683.1:935163-936905_minus NZ_CP019683.1:1558189-1559931_minus |
Campylobacter sputorum |
| 1101781 | 1,742 | NZ_CP018789.1:273370-275111_plus NZ_CP018789.1:1545743-1547484_minus |
Campylobacter sp. RM6137 |
| 7294871 | 1,742 | NZ_CP053828.1:357136-358877_plus NZ_CP053828.1:1667816-1669557_minus |
Campylobacter hyointestinalis |
| 1153931 | 1,742 | NZ_CP019685.1:577810-579551_plus NZ_CP019685.1:891862-893603_minus NZ_CP019685.1:1479764-1481505_minus |
Campylobacter sputorum |
| 1153921 | 1,740 | NZ_CP019684.1:614485-616224_plus NZ_CP019684.1:934958-936697_minus NZ_CP019684.1:1528990-1530729_minus |
Campylobacter sputorum |
| Archaea | |||
| 351728 | 3,604 | NC_016645.1:127214-130817_plus | Pyrobaculum ferrireducens |
| 28808 | 2,213 | NC_003364.1:1089640-1091852_plus | Pyrobaculum aerophilum |
| 37488 | 2,212 | NC_009376.1:623323-625534_minus | Pyrobaculum arsenaticum |
| 32288 | 2,202 | NC_000854.2:1218712-1220913_minus | Aeropyrum pernix |
| 40848 | 2,197 | NC_010525.1:690419-692615_plus | Pyrobaculum neutrophilum |
| 1145431 | 2,008 | NZ_CP019964.1:751297-753304_minus | Candidatus Mancarchaeum acidiphilum |
| 9220081 | 2,003 | NZ_CP060530.1:203642-205644_minus | Candidatus Micrarchaeum sp. |
| 39388 | 1,679 | NC_009954.1:129150-130828_minus | Caldivirga maquilingensis |
| 127981 | 1,650 | NC_022521.1:1165168-1166817_minus | Aeropyrum camini |
| 304318 | 1,576 | NC_015931.1:84671-86246_minus | Pyrolobus fumarii |
| Assembly ID | Gene length (bp) | RiboGrove Sequence ID (SeqID) | Organism |
|---|---|---|---|
| Bacteria | |||
| 44428 | 1,448 | NC_012982.1:2336679-2338126_minus | Hirschia baltica |
| 1460951 | 1,449 | NZ_CP021913.1:2386837-2388285_plus NZ_CP021913.1:3597920-3599368_plus |
Sagittula sp. P11 |
| 860061 | 1,451 | NZ_CP017718.1:2304269-2305719_minus | Hyphomonas sp. Mor2 |
| 1163161 | 1,453 | NZ_CP022540.1:1369380-1370832_plus NZ_CP022540.1:2482480-2483932_plus |
Antarctobacter heliothermus |
| 6279751 | 1,454 | NZ_AP022337.1:267139-268592_plus NZ_AP022337.1:1420942-1422395_plus NZ_AP022337.1:3191208-3192661_minus |
Mameliella alba |
| 34128 | 1,455 | NC_008358.1:2818466-2819920_minus | Hyphomonas neptunium |
| 9503471 | 1,455 | NZ_CP022271.1:2407999-2409453_minus | Hyphomonas sp. KY3 |
| 8694041 | 1,458 | NZ_CP060436.1:2482207-2483664_minus | Pseudooceanicola algae |
| 9217271 | 1,459 | NZ_CP069004.1:3093411-3094869_plus | Sulfitobacter mediterraneus |
| 8738751 | 1,459 | NZ_CP065429.1:477373-478831_plus | Sulfitobacter sp. B30-2 |
| 8872011 | 1,459 | NZ_CP065915.1:2729819-2731277_minus NZ_CP065915.1:3593071-3594529_minus |
Pelagovum pacificum |
| 1078381 | 1,459 | NZ_CP020612.1:582021-583479_minus NZ_CP020612.1:1166317-1167775_minus |
Paracoccus contaminans |
| Archaea | |||
| 39048 | 1,439 | NC_009776.1:728362-729800_plus | Ignicoccus hospitalis |
| 10131521 | 1,457 | NZ_LR792632.1:542755-544211_plus | Methanocaldococcus sp. SG7 |
| 2220501 | 1,463 | NZ_CP034692.1:397753-399215_minus | Halorubrum sp. BOL3-1 |
| 34548 | 1,466 | NC_007796.1:39814-41279_plus NC_007796.1:1301079-1302544_minus NC_007796.1:3501525-3502990_minus NC_007796.1:3507609-3509074_minus |
Methanospirillum hungatei |
| 10123301 | 1,466 | NZ_CP075546.1:133354-134819_plus NZ_CP075546.1:825954-827419_plus NZ_CP075546.1:872641-874106_plus NZ_CP075546.1:1727419-1728884_plus |
Methanospirillum sp. J.3.6.1-F.2.7.3 |
| 599268 | 1,466 | NC_020913.1:283607-285072_plus | Candidatus Methanomethylophilus alvus |
| 2068141 | 1,466 | NZ_CP017686.1:283608-285073_plus | Candidatus Methanomethylophilus alvus |
| 4352521 | 1,466 | NZ_LR699000.1:283607-285072_plus | Candidatus Methanomethylophilus alvus |
| 7330651 | 1,466 | NZ_CP058334.1:1530622-1532087_minus | Natronomonas halophila |
| 247941 | 1,467 | NZ_AP011526.1:3353-4819_minus NZ_AP011526.1:35473-36939_minus |
Methanococcus maripaludis |
| 42948 | 1,467 | NC_011832.1:754052-755518_plus NC_011832.1:1211333-1212799_plus NC_011832.1:1730673-1732139_minus |
Methanosphaerula palustris |
| 38328 | 1,467 | NC_009637.1:958998-960464_minus NC_009637.1:964038-965504_minus NC_009637.1:996345-997811_minus |
Methanococcus maripaludis |
| 6383091 | 1,467 | NZ_CP050014.1:2678648-2680114_minus | Haloarcula sp. JP-L23 |
| 255868 | 1,467 | NC_014222.1:1534651-1536117_minus NC_014222.1:1574464-1575930_plus |
Methanococcus voltae |
| 37228 | 1,467 | NC_009135.1:1594064-1595530_plus NC_009135.1:1628711-1630177_plus NC_009135.1:1633754-1635220_plus |
Methanococcus maripaludis |
| 39568 | 1,467 | NC_009975.1:859135-860601_plus NC_009975.1:891445-892911_plus NC_009975.1:896486-897952_plus |
Methanococcus maripaludis |
| 38268 | 1,467 | NC_009634.1:153-1619_plus NC_009634.1:1041673-1043139_minus NC_009634.1:1213597-1215063_plus NC_009634.1:1245383-1246849_plus |
Methanococcus vannielii |
| 7330661 | 1,467 | NZ_CP058335.1:2244804-2246270_minus | Natronomonas salina |
| 247951 | 1,467 | NZ_AP011528.1:3353-4819_minus NZ_AP011528.1:53932-55398_minus |
Methanococcus maripaludis |
| 32708 | 1,467 | NC_005791.1:3353-4819_minus NC_005791.1:8394-9860_minus NC_005791.1:40485-41951_minus |
Methanococcus maripaludis |
| 652801 | 1,467 | NZ_LT158599.1:571624-573090_plus | Methanoculleus bourgensis |
| 45008 | 1,467 | NC_007426.1:214463-215929_minus | Natronomonas pharaonis |
| 516578 | 1,467 | NC_019943.1:544798-546264_plus | Methanoregula formicica |
| 1547621 | 1,467 | NZ_CP026309.1:14431-15897_plus NZ_CP026309.1:2175095-2176561_minus |
Salinigranum rubrum |
| 1589601 | 1,467 | NZ_CP026606.1:983690-985156_plus NZ_CP026606.1:1015816-1017282_plus NZ_CP026606.1:1020857-1022323_plus |
Methanococcus maripaludis |
| 295728 | 1,467 | NC_015847.1:3353-4819_minus NC_015847.1:35451-36917_minus |
Methanococcus maripaludis |
| 127991 | 1,467 | NC_020388.1:26181-27647_plus | Natronomonas moolapensis |
| 1678381 | 1,467 | NZ_CP020120.1:3353-4819_minus NZ_CP020120.1:53932-55398_minus |
Methanococcus maripaludis |
| 319111 | 1,467 | NC_018227.2:565062-566528_plus | Methanoculleus bourgensis |
| Assembly ID | Copy number | Organism | |
|---|---|---|---|
| Bacteria | |||
| 1115491 | 37 | Tumebacillus avium | |
| 1166771 | 27 | Tumebacillus algifaecis | |
| 6720751 | 21 | Priestia megaterium | |
| 9972261 | 20 | Moritella sp. 5 | |
| 9972251 | 20 | Moritella sp. 28 | |
| 9972241 | 20 | Moritella sp. 36 | |
| 2023811 | 19 | Metabacillus litoralis | |
| 9972131 | 18 | Moritella sp. 24 | |
| 9513491 | 18 | Photobacterium ganghwense | |
| 2201351 | 18 | Peribacillus asahii | |
| Archaea | |||
| 2580821 | 5 | Natronorubrum bangense | |
| 5073821 | 5 | Natronorubrum aibiense | |
| 10123301 | 4 | Methanospirillum sp. J.3.6.1-F.2.7.3 | |
| 9298621 | 4 | Haloterrigena salifodinae | |
| 9962651 | 4 | Haloarcula sinaiiensis | |
| 521038 | 4 | Natronococcus occultus | |
| 4349641 | 4 | Methanosphaera stadtmanae | |
| 34548 | 4 | Methanospirillum hungatei | |
| 33648 | 4 | Methanosphaera stadtmanae | |
| 38268 | 4 | Methanococcus vannielii | |
| Assembly ID | Sum of entropy * (bits) | Mean entropy * (bits) | Number of variable positions | Gene copy number | Organism |
|---|---|---|---|---|---|
| Bacteria | |||||
| 4155511 | 226.25 | 0.13 | 247 | 12 | Sporomusa termitida |
| 7294871 | 217.64 | 0.12 | 237 | 3 | Campylobacter hyointestinalis |
| 1101781 | 211.21 | 0.12 | 230 | 3 | Campylobacter sp. RM6137 |
| 9010851 | 184.58 | 0.12 | 201 | 3 | Sinorhizobium meliloti |
| 8227731 | 167.21 | 0.10 | 216 | 5 | Klebsiella pneumoniae |
| 1469691 | 145.25 | 0.10 | 156 | 3 | Olleya sp. Bg11-27 |
| 7292581 | 136.25 | 0.09 | 145 | 4 | Microbulbifer sp. YPW1 |
| 638441 | 135.84 | 0.08 | 138 | 4 | Selenomonas sp. oral taxon 136 |
| 9428571 | 122.06 | 0.08 | 123 | 4 | Thermobispora bispora |
| 9307231 | 117.00 | 0.08 | 117 | 2 | Thermoleptolyngbya sp. PKUAC-SCTB121 |
| Archaea | |||||
| 4982121 | 137.00 | 0.09 | 137 | 2 | Halomicrobium sp. ZPS1 ** |
| 2582391 | 125.81 | 0.09 | 137 | 3 | Halomicrobium mukohataei |
| 999901 | 98.00 | 0.07 | 98 | 2 | Halorientalis sp. IM1011 |
| 8834941 | 97.00 | 0.07 | 97 | 2 | Halosimplex litoreum |
| 5205301 | 88.16 | 0.06 | 96 | 3 | Halomicrobium sp. LC1Hm |
| 2835121 | 78.06 | 0.05 | 85 | 3 | Haloarcula marismortui |
| 247521 | 72.55 | 0.05 | 79 | 3 | Haloarcula sp. CBA1115 |
| 9962651 | 67.78 | 0.05 | 82 | 4 | Haloarcula sinaiiensis |
| 1492601 | 66.00 | 0.04 | 66 | 2 | Haloarcula taiwanensis |
| 2220501 | 27.05 | 0.02 | 28 | 3 | Halorubrum sp. BOL3-1 |
* 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