Update to release 14.7

Fix #1
Rfam · Mar 11, 2022 · 9cb1eb8 · 9cb1eb8
1 parent e7521d5
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diff --git a/Readme.md b/Readme.md
@@ -1,12 +1,12 @@
 # Rfam Taxonomy
 
+Based on **Rfam 14.7** (December 2021). See [releases](https://github.com/Rfam/rfam-taxonomy/releases) for previous versions.
+
 This repository contains the code and data for analysing the taxonomic distribution
 of the [Rfam](https://rfam.org) families. The goal is to identify domain-specific
 subsets of Rfam covariance models for annotating bacterial, eukaryotic,
 and other genomes with the [Infernal](http://eddylab.org/infernal) software.
 
-The current analysis is based on **Rfam 14.6** (July 2021). The data should be updated after every Rfam release.
-
 The code uses the Rfam [public MySQL database](https://rfam.readthedocs.io/en/latest/database.html)
 to compare the taxonomic domains of sequences from the manually curated
 [seed alignments](https://rfam.readthedocs.io/en/latest/glossary.html)
@@ -16,7 +16,7 @@ and the automatically identified [full region](https://rfam.readthedocs.io/en/la
 Each file contains seven columns:
 
 1. `Family` = Rfam accession (e.g. RF00001)
-2. `Domain` = Taxonomic domain where the family is found
+2. `Domain` = Taxonomic domain where the family is found (:grey_exclamation: this is the most important column)
 3. `Seed domains` = All taxonomic domains from the seed alignment
 4. `Full region domains` = All taxonomic domains from full region hits
 5. `Rfam ID` = Rfam identifier (e.g. 5S_rRNA)
@@ -74,21 +74,36 @@ source ENV/bin/activate
 pip install -r requirements.txt
 ```
 
-## Usage
+## Updating the data
 
-```
-# when running for the first time:
-python rfam-taxonomy.py --precompute-full
-python rfam-taxonomy.py --precompute-seed
+After each Rfam release, the data in this repo need to be updated locally and
+pushed to GitHub.
 
-# after precompute is done, run:
-python rfam-taxonomy.py
+1. Generate new data
 
-# to see additional options:
-python rfam-taxonomy.py --help
-```
+    ```
+    # when running for the first time (needs to run in this order):
+    python rfam-taxonomy.py --precompute-full
+    python rfam-taxonomy.py --precompute-seed
+
+    # after precompute is done, run:
+    python rfam-taxonomy.py
+
+    # to see additional options:
+    python rfam-taxonomy.py --help
+    ```
+
+1. Review the changes
+
+    The results must be manually reviewed before committing the new files by checking the difference between the old and the new versions using git.
+
+    It is normal for the values in the 3rd and 4th columns to change but `Domain`, the 2nd column, should stay stable unless the affected family has been significantly updated.
+
+1. Update release info in Readme
+
+1. Create new GitHub release
 
 ## Feedback
 
-Feel free to create GitHub issues to ask questions or provide feedback.
+Feel free to create [GitHub issues](https://github.com/Rfam/rfam-taxonomy/issues) to ask questions or provide feedback.
 Pull requests are also welcome.
diff --git a/domains/Readme.md b/domains/Readme.md
@@ -3,17 +3,17 @@
 The number of Rfam families observed in different domains:
 
 ```
-2486 Eukaryota
- 911 Bacteria
+2482 Eukaryota
+ 913 Bacteria
  181 Viruses
  118 Bacteria/Mixed
   99 Archaea
-  77 Eukaryota/Mixed
-  73 unclassified sequences
+  76 Eukaryota/Mixed
+  72 unclassified sequences
   29 unclassified sequences/Bacteria
   26 Viruses/Mixed
   24 Mixed
-  13 unclassified sequences/Mixed
+  16 unclassified sequences/Mixed
   12 Mixed/Bacteria
    7 Archaea/Mixed
    4 Mixed/Eukaryota

diff --git a/domains/all-domains.csv b/domains/all-domains.csv
diff --git a/domains/bacteria.csv b/domains/bacteria.csv
@@ -9,7 +9,7 @@ RF00018,Bacteria,Bacteria (100.0%),"Bacteria (96.44%), Eukaryota (3.56%)",CsrB,C
 RF00021,Bacteria,Bacteria (100.0%),"Bacteria (96.63%), Eukaryota (3.37%)",Spot_42,Spot 42 RNA,Gene; sRNA;
 RF00022,Bacteria,Bacteria (100.0%),"Bacteria (96.58%), Eukaryota (3.42%)",GcvB,GcvB RNA,Gene;
 RF00023,Bacteria,"Bacteria (93.92%), unclassified sequences (3.77%), Eukaryota (2.1%), Viruses (0.21%)","Bacteria (98.65%), Eukaryota (0.84%), unclassified sequences (0.28%), Viruses (0.2%), Archaea (0.03%)",tmRNA,transfer-messenger RNA,Gene;
-RF00033,Bacteria,Bacteria (100.0%),"Bacteria (95.35%), Eukaryota (4.65%)",MicF,MicF RNA,Gene; antisense;
+RF00033,Bacteria,Bacteria (100.0%),"Bacteria (97.37%), Eukaryota (2.63%)",MicF,MicF RNA,Gene; antisense;
 RF00034,Bacteria,"Bacteria (92.31%), unclassified sequences (7.69%)","Bacteria (94.9%), Eukaryota (4.08%), unclassified sequences (1.02%)",RprA,RprA RNA,Gene; sRNA;
 RF00035,Bacteria,Bacteria (100.0%),Bacteria (100.0%),OxyS,OxyS RNA,Gene; sRNA;
 RF00038,Bacteria,Bacteria (100.0%),Bacteria (100.0%),PrfA,PrfA thermoregulator UTR,Cis-reg; thermoregulator;
@@ -21,7 +21,7 @@ RF00050,Bacteria,"Bacteria (97.24%), unclassified sequences (2.07%), Other (0.69
 RF00057,Bacteria,"Bacteria (96.15%), unclassified sequences (3.85%)","Bacteria (96.17%), Eukaryota (3.48%), unclassified sequences (0.35%)",RyhB,RyhB RNA,Gene; sRNA;
 RF00059,Mixed/Bacteria,"Bacteria (85.09%), Eukaryota (9.65%), Other (2.63%), Archaea (1.75%), unclassified sequences (0.88%)","Bacteria (91.81%), Eukaryota (7.86%), Archaea (0.31%), Other (0.02%)",TPP,TPP riboswitch (THI element),Cis-reg; riboswitch;
 RF00077,Bacteria,Bacteria (100.0%),Bacteria (100.0%),SraB,SraB RNA,Gene; sRNA;
-RF00078,Bacteria,Bacteria (100.0%),"Bacteria (95.59%), Eukaryota (4.41%)",MicA,MicA sRNA,Gene; sRNA;
+RF00078,Bacteria,Bacteria (100.0%),"Bacteria (95.0%), Eukaryota (5.0%)",MicA,MicA sRNA,Gene; sRNA;
 RF00079,Bacteria,"Bacteria (91.3%), unclassified sequences (8.7%)","Bacteria (92.9%), Eukaryota (5.92%), unclassified sequences (1.18%)",OmrA-B,OmrA-B family,Gene; sRNA;
 RF00080,Bacteria,"Bacteria (89.66%), unclassified sequences (10.34%)","Bacteria (98.2%), Eukaryota (1.44%), unclassified sequences (0.36%)",yybP-ykoY,yybP-ykoY manganese riboswitch,Cis-reg; riboswitch;
 RF00081,Bacteria,Bacteria (100.0%),"Bacteria (95.71%), Eukaryota (4.29%)",ArcZ,ArcZ RNA,Gene; sRNA;
@@ -67,7 +67,7 @@ RF00240,Bacteria/Mixed,Bacteria (100.0%),"Bacteria (56.52%), Eukaryota (43.48%)"
 RF00242,Bacteria,Bacteria (100.0%),"Bacteria (93.94%), Eukaryota (6.06%)",ctRNA_pT181,ctRNA,Gene; antisense;
 RF00243,Bacteria,Bacteria (100.0%),"Bacteria (92.86%), Eukaryota (7.14%)",traJ_5,traJ 5' UTR,Cis-reg;
 RF00368,Bacteria,"Bacteria (93.75%), unclassified sequences (6.25%)","Bacteria (93.02%), Eukaryota (5.81%), unclassified sequences (1.16%)",sroB,sroB RNA,Gene; sRNA;
-RF00369,Bacteria,"Bacteria (83.33%), unclassified sequences (16.67%)","Bacteria (93.75%), Eukaryota (4.69%), unclassified sequences (1.56%)",sroC,sroC RNA,Gene; sRNA;
+RF00369,Bacteria,"Bacteria (83.33%), unclassified sequences (16.67%)","Bacteria (94.83%), Eukaryota (5.17%)",sroC,sroC RNA,Gene; sRNA;
 RF00370,Bacteria,Bacteria (100.0%),"Bacteria (95.35%), Eukaryota (4.65%)",sroD,sroD RNA,Gene; sRNA;
 RF00371,Bacteria,"Bacteria (75.0%), unclassified sequences (25.0%)","Bacteria (92.11%), Eukaryota (5.26%), unclassified sequences (2.63%)",sroE,sroE RNA,Gene; sRNA;
 RF00372,Bacteria/Mixed,Bacteria (100.0%),"Bacteria (87.5%), Eukaryota (12.5%)",sroH,sroH RNA,Gene; sRNA;
@@ -289,6 +289,7 @@ RF01700,Bacteria/Mixed,"unclassified sequences (66.67%), Bacteria (33.33%)","Bac
 RF01701,Bacteria,"unclassified sequences (66.79%), Bacteria (33.21%)","Bacteria (66.16%), unclassified sequences (33.84%)",Cyano-1,Cyano-1 RNA,Gene; sRNA;
 RF01702,Bacteria/Mixed,"unclassified sequences (82.46%), Bacteria (17.54%)","unclassified sequences (71.21%), Bacteria (27.27%), Eukaryota (1.52%)",Cyano-2,Cyano-2 RNA,Gene; sRNA;
 RF01703,Bacteria,Bacteria (100.0%),Bacteria (100.0%),Dictyoglomi-1,Dictyoglomi-1 RNA,Gene; sRNA;
+RF01704,Bacteria/Mixed,"unclassified sequences (78.67%), Bacteria (21.33%)","unclassified sequences (66.67%), Bacteria (30.16%), Viruses (2.95%), Eukaryota (0.23%)",Downstream-peptide,Downstream peptide RNA,Cis-reg;
 RF01705,Bacteria,"Bacteria (67.66%), unclassified sequences (32.34%)","Bacteria (97.54%), Eukaryota (1.25%), unclassified sequences (1.21%)",Flavo-1,Flavo-1 RNA,Gene; sRNA;
 RF01707,Bacteria,Bacteria (100.0%),"Bacteria (96.23%), Eukaryota (3.77%)",JUMPstart,JUMPstart RNA,Cis-reg;
 RF01708,Bacteria,Bacteria (100.0%),"Bacteria (99.02%), Eukaryota (0.98%)",L17DE,L17 ribosomal protein downstream element,Cis-reg;
@@ -300,20 +301,20 @@ RF01713,Bacteria,Bacteria (100.0%),Bacteria (100.0%),Moco-II,Moco-II RNA,Cis-reg
 RF01715,Bacteria,Bacteria (100.0%),Bacteria (100.0%),Pedo-repair,Pedo-repair RNA,Cis-reg;
 RF01716,Bacteria,"unclassified sequences (70.77%), Bacteria (29.23%)","unclassified sequences (59.74%), Bacteria (40.26%)",PhotoRC-I,PhotoRC-I RNA,Cis-reg;
 RF01718,unclassified sequences/Bacteria,"unclassified sequences (93.75%), Bacteria (6.25%)","unclassified sequences (83.33%), Bacteria (16.67%)",Polynucleobacter-1,Polynucleobacter-1 RNA,Gene; sRNA;
-RF01719,Bacteria,Bacteria (100.0%),"Bacteria (98.95%), Eukaryota (1.05%)",Pseudomon-1,Pseudomon-1/ErsA RNA,Gene; sRNA;
+RF01719,Bacteria,Bacteria (100.0%),"Bacteria (93.0%), unclassified sequences (6.0%), Eukaryota (1.0%)",Pseudomon-1,Pseudomon-1/ErsA RNA,Gene; sRNA;
 RF01720,Bacteria,Bacteria (100.0%),"Bacteria (97.78%), Eukaryota (2.22%)",Pseudomon-Rho,Pseudomon-Rho RNA,Cis-reg;
 RF01721,Bacteria,Bacteria (100.0%),Bacteria (100.0%),Pseudomon-groES,Pseudomon-groES RNA,Cis-reg;
 RF01723,Bacteria,Bacteria (100.0%),Bacteria (100.0%),Rhizobiales-2,Rhizobiales-2 RNA,Gene; sRNA;
 RF01724,Bacteria/Mixed,Bacteria (100.0%),"Bacteria (88.46%), Eukaryota (11.54%)",SAM-Chlorobi,SAM-Chlorobi RNA,Cis-reg;
 RF01726,Bacteria/Mixed,"unclassified sequences (80.95%), Bacteria (19.05%)","Bacteria (81.3%), unclassified sequences (17.5%), Eukaryota (1.2%)",SAM-II_long_loops,SAM-II long loop,Cis-reg;
 RF01727,Bacteria/Mixed,"unclassified sequences (50.94%), Bacteria (49.06%)","Bacteria (88.45%), unclassified sequences (10.76%), Eukaryota (0.8%)",SAM-SAH,SAM/SAH riboswitch,Cis-reg; riboswitch;
-RF01728,Bacteria/Mixed,Bacteria (100.0%),"Bacteria (86.39%), Eukaryota (13.61%)",STAXI,STAXI RNA,Gene; sRNA;
+RF01728,Bacteria/Mixed,"Bacteria (95.35%), unclassified sequences (4.65%)","Bacteria (86.41%), Eukaryota (12.14%), unclassified sequences (1.46%)",STAXI,STAXI RNA,Gene; sRNA;
 RF01729,unclassified sequences/Bacteria,unclassified sequences (100.0%),"unclassified sequences (86.67%), Bacteria (13.33%)",Termite-flg,Termite-flg RNA,Cis-reg;
 RF01731,Bacteria/Mixed,"unclassified sequences (86.67%), Bacteria (13.33%)","Bacteria (87.37%), unclassified sequences (12.22%), Eukaryota (0.4%)",TwoAYGGAY,TwoAYGGAY RNA,Cis-reg;
 RF01732,Bacteria,Bacteria (100.0%),"Bacteria (96.34%), unclassified sequences (3.66%)",asd,MarS sRNA,Gene; sRNA;
 RF01733,Bacteria,Bacteria (100.0%),Bacteria (100.0%),atoC,atoC RNA,Cis-reg;
-RF01734,Mixed/Bacteria,"Bacteria (79.44%), unclassified sequences (11.85%), Archaea (8.71%)","Bacteria (92.61%), Archaea (5.1%), unclassified sequences (1.59%), Eukaryota (0.7%)",Fluoride,Fluoride riboswitch,Cis-reg; riboswitch;
-RF01735,Bacteria,Bacteria (100.0%),"Bacteria (99.58%), Eukaryota (0.42%)",epsC,epsC RNA,Cis-reg;
+RF01734,Mixed/Bacteria,"Bacteria (80.45%), unclassified sequences (11.9%), Archaea (7.65%)","Bacteria (92.39%), Archaea (5.06%), unclassified sequences (1.78%), Eukaryota (0.73%), Other (0.05%)",Fluoride,Fluoride riboswitch,Cis-reg; riboswitch;
+RF01735,Bacteria,"Bacteria (90.0%), unclassified sequences (10.0%)","Bacteria (97.97%), unclassified sequences (1.63%), Eukaryota (0.41%)",epsC,epsC RNA,Cis-reg;
 RF01736,Bacteria,Bacteria (100.0%),Bacteria (100.0%),flg-Rhizobiales,flg-Rhizobiales RNA,Cis-reg;
 RF01738,Bacteria,Bacteria (100.0%),Bacteria (100.0%),gabT,gabT RNA,Cis-reg;
 RF01740,Bacteria,Bacteria (100.0%),"Bacteria (98.08%), Eukaryota (1.92%)",gyrA,gyrA RNA,Cis-reg;
@@ -324,17 +325,17 @@ RF01746,Bacteria,"Bacteria (55.56%), unclassified sequences (44.44%)","Bacteria
 RF01747,Bacteria/Mixed,"unclassified sequences (81.67%), Bacteria (18.33%)","Bacteria (87.05%), unclassified sequences (12.69%), Eukaryota (0.26%)",msiK,msiK RNA,Cis-reg;
 RF01748,Bacteria/Mixed,Bacteria (100.0%),"Bacteria (87.88%), Eukaryota (12.12%)",nuoG,nuoG RNA,Cis-reg;
 RF01749,Bacteria,Bacteria (100.0%),Bacteria (100.0%),pan,pan motif,Cis-reg;
-RF01750,Bacteria,"Bacteria (54.95%), unclassified sequences (45.05%)","Bacteria (94.98%), unclassified sequences (4.9%), Eukaryota (0.12%)",ZMP-ZTP,ZMP/ZTP riboswitch,Cis-reg; riboswitch;
+RF01750,Bacteria,"Bacteria (58.19%), unclassified sequences (41.81%)","Bacteria (96.17%), unclassified sequences (3.62%), Eukaryota (0.1%), Other (0.1%)",ZMP-ZTP,ZMP/ZTP riboswitch,Cis-reg; riboswitch;
 RF01752,Bacteria,"unclassified sequences (61.29%), Bacteria (38.71%)","Bacteria (57.78%), unclassified sequences (42.22%)",psaA,psaA RNA,Cis-reg;
 RF01753,Bacteria,"unclassified sequences (69.23%), Bacteria (30.77%)","unclassified sequences (57.45%), Bacteria (42.55%)",psbNH,psbNH RNA,Cis-reg;
-RF01754,Bacteria,Bacteria (100.0%),"Bacteria (98.92%), Eukaryota (1.08%)",radC,radC RNA,Cis-reg;
+RF01754,Bacteria,"Bacteria (84.46%), unclassified sequences (15.54%)","Bacteria (94.93%), unclassified sequences (4.02%), Eukaryota (1.05%)",radC,radC RNA,Cis-reg;
 RF01755,Bacteria,Bacteria (100.0%),"Bacteria (98.86%), Eukaryota (1.14%)",rmf,rmf RNA,Cis-reg;
 RF01756,Bacteria,Bacteria (100.0%),"Bacteria (98.89%), Eukaryota (1.11%)",rne-II,rne-II RNA,Cis-reg;
 RF01757,Bacteria,Bacteria (100.0%),Bacteria (100.0%),sbcD,sbcD RNA,Gene; sRNA;
 RF01758,Bacteria,Bacteria (100.0%),"Bacteria (98.89%), Eukaryota (1.11%)",sucA-II,sucA-II RNA,Cis-reg;
 RF01759,Bacteria,Bacteria (100.0%),"Bacteria (98.77%), Eukaryota (1.23%)",sucC,sucC RNA,Cis-reg;
 RF01760,Mixed/Bacteria,"Bacteria (70.21%), unclassified sequences (23.4%), Other (6.38%)","Bacteria (92.0%), unclassified sequences (5.5%), Other (1.5%), Eukaryota (1.0%)",traJ-II,traJ-II RNA,Cis-reg;
-RF01763,Bacteria,Bacteria (100.0%),"Bacteria (99.7%), Eukaryota (0.3%)",ykkC-III,Guanidine-III riboswitch,Cis-reg;
+RF01763,Bacteria,"Bacteria (90.7%), unclassified sequences (9.3%)","Bacteria (99.11%), unclassified sequences (0.59%), Eukaryota (0.3%)",ykkC-III,Guanidine-III riboswitch,Cis-reg;
 RF01764,Bacteria,Bacteria (100.0%),Bacteria (100.0%),yjdF,yjdF RNA,Cis-reg;
 RF01766,Bacteria,Bacteria (100.0%),"Bacteria (97.8%), Eukaryota (2.2%)",cspA,cspA thermoregulator,Cis-reg; thermoregulator;
 RF01767,Bacteria,Bacteria (100.0%),Bacteria (100.0%),SMK_box_riboswitch,SMK box translational riboswitch (SAM-III),Cis-reg; riboswitch;
@@ -404,8 +405,7 @@ RF02005,Mixed/Bacteria,"Bacteria (54.02%), unclassified sequences (45.4%), Other
 RF02029,Bacteria,Bacteria (100.0%),"Bacteria (95.0%), Eukaryota (5.0%)",sraA,sraA,Gene; sRNA;
 RF02030,Bacteria,"Bacteria (95.83%), unclassified sequences (4.17%)","Bacteria (95.31%), Eukaryota (3.91%), unclassified sequences (0.78%)",tp2,tp2,Gene; sRNA;
 RF02031,Bacteria,Bacteria (100.0%),"Bacteria (95.39%), Eukaryota (4.61%)",tpke11,tpke11,Gene; sRNA;
-RF02032,Bacteria/Mixed,"unclassified sequences (80.0%), Bacteria (20.0%)","unclassified sequences (45.9%), Bacteria (37.7%), Viruses (16.39%)",GOLLD,"Giant, ornate, lake- and Lactobacillales-derived (GOLLD) RNA",Gene;
-RF02033,Mixed/Bacteria,"Bacteria (85.45%), Archaea (9.09%), unclassified sequences (4.55%), Viruses (0.91%)","Bacteria (93.96%), Archaea (5.16%), unclassified sequences (0.44%), Viruses (0.26%), Eukaryota (0.17%)",HEARO,HNH endonuclease-associated RNA and ORF (HEARO) RNA,Gene;
+RF02033,Mixed/Bacteria,"Bacteria (85.61%), unclassified sequences (12.95%), Viruses (0.72%), Archaea (0.72%)","Bacteria (92.47%), Archaea (5.82%), unclassified sequences (1.4%), Viruses (0.23%), Eukaryota (0.08%)",HEARO,HNH endonuclease-associated RNA and ORF (HEARO) RNA,Gene;
 RF02048,Bacteria,Bacteria (100.0%),Bacteria (100.0%),STnc30,Salmonella enterica conserved region STnc30,Gene; sRNA;
 RF02049,Bacteria,Bacteria (100.0%),Bacteria (100.0%),STnc460,Salmonella enterica sRNA STnc460,Gene; sRNA;
 RF02050,Bacteria,Bacteria (100.0%),Bacteria (100.0%),STnc470,Salmonella enterica sRNA STnc470,Gene; sRNA;
@@ -583,7 +583,7 @@ RF02496,Bacteria,"Bacteria (87.88%), unclassified sequences (12.12%)","Bacteria
 RF02497,Bacteria/Mixed,Bacteria (100.0%),"Bacteria (83.33%), Eukaryota (16.67%)",Atu_C10,Rhizobiales sRNA Atu_C10,Gene; sRNA;
 RF02498,Bacteria/Mixed,Bacteria (100.0%),"Bacteria (75.0%), Eukaryota (25.0%)",Atu_C3,Rhizobiales sRNA Atu_C3,Gene; sRNA;
 RF02499,Bacteria/Mixed,Bacteria (100.0%),"Bacteria (75.0%), Eukaryota (25.0%)",Atu_C4,Rhizobiales sRNA Atu_C4,Gene; sRNA;
-RF02500,Bacteria,"Bacteria (87.5%), unclassified sequences (12.5%)","Bacteria (97.17%), unclassified sequences (1.89%), Eukaryota (0.94%)",Atu_C6,EcpR1,Gene; sRNA;
+RF02500,Bacteria,"Bacteria (87.5%), unclassified sequences (12.5%)","Bacteria (98.89%), Eukaryota (1.11%)",Atu_C6,EcpR1,Gene; sRNA;
 RF02501,Bacteria,"Bacteria (66.67%), unclassified sequences (33.33%)","Bacteria (96.0%), Eukaryota (2.0%), unclassified sequences (2.0%)",Atu_C7,Rhizobiales sRNA Atu_C7,Gene; sRNA;
 RF02502,Bacteria,"Bacteria (92.59%), unclassified sequences (7.41%)","Bacteria (97.94%), Eukaryota (1.03%), unclassified sequences (1.03%)",Atu_C8,Rhizobiales sRNA Atu_C8,Gene; sRNA;
 RF02503,Bacteria,Bacteria (100.0%),"Bacteria (97.33%), Eukaryota (2.67%)",Atu_C9,Rhizobiales sRNA Atu_C9,Gene; sRNA;
@@ -758,7 +758,7 @@ RF02751,Bacteria,Bacteria (100.0%),"Bacteria (90.91%), Eukaryota (9.09%)",ES036,
 RF02752,Bacteria,Bacteria (100.0%),Bacteria (100.0%),ES056,ES056 sRNA,Gene; sRNA;
 RF02753,Bacteria,Bacteria (100.0%),Bacteria (100.0%),ES173,ES173 sRNA,Gene; sRNA;
 RF02754,Bacteria/Mixed,Bacteria (100.0%),"Bacteria (87.5%), Eukaryota (12.5%)",ES205,ES205 sRNA,Gene; sRNA;
-RF02755,Bacteria,Bacteria (100.0%),"Bacteria (96.55%), Eukaryota (3.45%)",ES222,ES222 sRNA,Gene; sRNA;
+RF02755,Bacteria,Bacteria (100.0%),"Bacteria (95.83%), Eukaryota (4.17%)",ES222,ES222 sRNA,Gene; sRNA;
 RF02756,Bacteria/Mixed,Bacteria (100.0%),"Bacteria (87.5%), Eukaryota (12.5%)",ES239,ES239 sRNA,Gene; sRNA;
 RF02757,Bacteria,Bacteria (100.0%),"Bacteria (97.14%), Eukaryota (2.86%)",Erse,Erse small RNA,Gene; sRNA;
 RF02758,Bacteria,Bacteria (100.0%),Bacteria (100.0%),RhlA_thermometer,RhlA 5' UTR ROSE like thermometer,Cis-reg; thermoregulator;
@@ -854,7 +854,7 @@ RF02868,Bacteria,Bacteria (100.0%),Bacteria (100.0%),ncS037,Burkholderia sRNA 37
 RF02869,Mixed/Bacteria,"Bacteria (75.0%), Eukaryota (25.0%)","Bacteria (98.21%), Eukaryota (1.79%)",ncS025,Burkholderia sRNA 25,Gene; sRNA;
 RF02870,Bacteria,Bacteria (100.0%),Bacteria (100.0%),ncS035,Burkholderia sRNA 35,Gene; sRNA;
 RF02871,Bacteria,Bacteria (100.0%),"Bacteria (98.95%), Eukaryota (1.05%)",ncS54,Burkholderia sRNA 54,Gene; sRNA;
-RF02872,Bacteria,Bacteria (100.0%),"Bacteria (98.44%), Eukaryota (1.56%)",SrbA,sRNA regulator of biofilms A,Gene; sRNA;
+RF02872,Bacteria,Bacteria (100.0%),"Bacteria (98.36%), Eukaryota (1.64%)",SrbA,sRNA regulator of biofilms A,Gene; sRNA;
 RF02873,Bacteria/Mixed,Bacteria (100.0%),"Bacteria (75.0%), Eukaryota (25.0%)",AS-traI,Antisense to traI,Gene; antisense;
 RF02875,Bacteria,Bacteria (100.0%),Bacteria (100.0%),AS-pc01,Antisense to pHK01_035,Gene; antisense;
 RF02876,Bacteria/Mixed,Bacteria (100.0%),"Bacteria (75.0%), Eukaryota (25.0%)",AS-pc02,Antisense to pHK01_099,Gene; antisense;
@@ -1074,3 +1074,5 @@ RF04181,Bacteria,Bacteria (100.0%),Bacteria (100.0%),rteR,rteR sRNA,Gene; sRNA;
 RF04182,Bacteria,Bacteria (100.0%),Bacteria (100.0%),GibS,GibS sRNA,Gene; sRNA;
 RF04183,Bacteria,Bacteria (100.0%),"Bacteria (99.37%), Eukaryota (0.63%)",Bacteroidales_small_SRP,Bacteroidales small SRP,Gene;
 RF04184,Bacteria,Bacteria (100.0%),Bacteria (100.0%),BTnc060,Bacteroides sRNA BTnc060,Gene; sRNA;
+RF04189,Bacteria,Bacteria (100.0%),Bacteria (100.0%),icd-II,icd-II ncRNA motif,Cis-reg;
+RF04192,Bacteria,Bacteria (100.0%),Bacteria (100.0%),carA,carA ncRNA motif,Cis-reg;