- Sequence and structure-based ribosomal RNA alignments included with Ribovore
- Covariance model (CM) files that include a single CM and profile HMM
ribotyperversusriboalignermodelsribotyper.cma multi-model CM library file- Getting model statistics using Infernal's
cmstatprogram - CRW database reference
Ribovore includes models built from 18 different alignments. Seven of these derive from Rfam, and 11 were created during the course of Ribovore development.
These alignments were created using 1 of 2 strategies:
Build strategy 1: alignment and consensus secondary structure was determined using the CRW conversion strategy described in the SSU-ALIGN 0.1 user's guide (section 5) using tools/scripts available on GitHub. Sequence and structure information in these alignments derive from the CRW website/database (reference below).
Build strategy 2: initial version of the alignment and consensus secondary structure and model was determined using build strategy 1, but that model was used to create a new alignment and model using the Rfam model building pipeline (as of Rfam release 12.0), as follows:
- the model from build strategy 1 was used to search the Rfam database sequence database
Rfamseq(a large database consisting of much of the GenBank nucleotide database) - all resulting hits were filtered by removing highly similar sequences
- the suriviving hits were aligned to the model from build strategy 1
- the
cmbuildprogram of Infernal was used with the--refineoption to refine to get a final alignment and a new model was built from it
As you can see in the table below, the 7 Rfam alignments and 3 of the other alignments were created with build strategy 2. The other 7 alignments that used build strategy 1 have very few (< 5) sequences in them and should and will be updated in future versions. Models built from these 7 build strategy 1 alignments are less trustworthy and generally less useful than the other models built from build strategy 2 alignments.
| alignment file name | alignment build strategy | model files built from alignment | # seqs | model length | Rfam accession | Rfam DB release |
|---|---|---|---|---|---|---|
SSU_rRNA_archaea.RF01959.stk |
2 | rt.SSU_rRNA_archaea.enone.cm, ra.SSU_rRNA_archaea.edf.cm |
86 | 1477 | RF01959 | 12.2 |
SSU_rRNA_bacteria.RF00177.stk |
2 | rt.SSU_rRNA_bacteria.enone.cm, ra.SSU_rRNA_bacteria.edf.cm |
99 | 1533 | RF00177 | 12.2 |
SSU_rRNA_eukarya.RF01960.stk |
2 | rt.SSU_rRNA_eukarya.enone.cm, ra.SSU_rRNA_eukarya.edf.cm |
91 | 1851 | RF01960 | 12.2 |
SSU_rRNA_microsporidia.RF02542.stk |
2 | rt.SSU_rRNA_microsporidia.enone.cm, ra.SSU_rRNA_microsporidia.edf.cm |
46 | 1312 | RF02542 | 12.2 |
LSU_rRNA_archaea.RF02540.stk |
2 | rt.LSU_rRNA_archaea.enone.cm, ra.LSU_rRNA_archaea.edf.cm |
91 | 2990 | RF02540 | 12.2 |
LSU_rRNA_bacteria.RF02541.stk |
2 | rt.LSU_rRNA_bacteria.enone.cm, ra.LSU_rRNA_bacteria.edf.cm |
102 | 2925 | RF02541 | 12.2 |
LSU_rRNA_eukarya.RF02543.stk |
2 | rt.LSU_rRNA_eukarya.enone.cm, ra.LSU_rRNA_eukarya.edf.cm |
88 | 3401 | RF02543 | 12.2 |
SSU_rRNA_mitochondria_metazoa.stk |
2 | rt.SSU_rRNA_mitochondria_metazoa.enone.cm, ra.SSU_rRNA_mitochondria_metazoa.edf.cm |
83 | 954 | - | - |
SSU_rRNA_mitochondria_amoeba.stk |
1 | rt.SSU_rRNA_mitochondria_amoeba.enone.cm, ra.SSU_rRNA_mitochondria_amoeba.edf.cm |
2 | 1861 | - | - |
SSU_rRNA_mitochondria_chlorophyta.stk |
1 | rt.SSU_rRNA_mitochondria_chlorophyta.enone.cm, ra.SSU_rRNA_mitochondria_chlorophyta.edf.cm |
2 | 1200 | - | - |
SSU_rRNA_mitochondria_fungi.stk |
1 | rt.SSU_rRNA_mitochondria_fungi.enone.cm, ra.SSU_rRNA_mitochondria_fungi.edf.cm |
4 | 1603 | - | - |
SSU_rRNA_mitochondria_kinetoplast.stk |
1 | rt.SSU_rRNA_mitochondria_kinetoplast.enone.cm, ra.SSU_rRNA_mitochondria_kinetoplast.edf.cm |
3 | 624 | - | - |
SSU_rRNA_mitochondria_plant.stk |
1 | rt.SSU_rRNA_mitochondria_plant.enone.cm, ra.SSU_rRNA_mitochondria_plant.edf.cm |
4 | 1951 | - | - |
SSU_rRNA_mitochondria_protist.stk |
1 | rt.SSU_rRNA_mitochondria_protist.enone.cm, ra.SSU_rRNA_mitochondria_protist.edf.cm |
2 | 1677 | - | - |
SSU_rRNA_chloroplast.stk |
2 | rt.SSU_rRNA_chloroplast.enone.cm, ra.SSU_rRNA_chloroplast.edf.cm |
94 | 1488 | - | - |
SSU_rRNA_chloroplast_pilostyles.stk |
1 | rt.SSU_rRNA_chloroplast_pilostyles.enone.cm, ra.SSU_rRNA_chloroplast_pilostyles.edf.cm |
1 | 1531 | - | - |
SSU_rRNA_cyanobacteria.stk |
2 | rt.SSU_rRNA_cyanobacteria.enone.cm, ra.SSU_rRNA_cyanobacteria.edf.cm |
49 | 1487 | - | - |
SSU_rRNA_apicoplast.stk |
1 | rt.SSU_rRNA_apicoplast.enone.cm, ra.SSU_rRNA_apicoplast.edf.cm |
3 | 1463 | - | - |
All files listed in columns 1 and 3 can be found in the ribovore/models directory ($RIBOSCRIPTSDIR/models following installation).
The model files that begin with rt. contain ribotyper models and
those that begin with ra. contain riboaligner models. These models
were built differently. All ribotyper models were built using the
cmbuild program from Infernal
version 1.1.3 with command line options --p7ml --enone using the
alignment files listed in the table above. All riboaligner
models were built using the cmbuild program from
Infernal version 1.1.2 with default
parameters (no command line options) using the aligment files listed
in the table above. The riboaligner models were built with
cmbuild's entropy weighting feature that controls the average
entropy per model position~\cite{Karplus98,Nawrocki09b}, and the
ribotyper models were built with this feature turned off. Additionally
the ribotyper models were built such that the profile HMM used for
filtering was built to be maximally similar to the CM (the --p7ml
option). These options were selected because they increased
classification accuracy on our internal testing for ribotyper. Default
cmbuild built models are provided for riboaligner because those
models were more accurate on prediction alignment endpoints correctly
in our testing.
The ribotyper.cm file is a CM library of all models that begin with
rt in the above table. This file is used in the first
stage of ribotyper to classify sequences.
Getting model statistics using Infernal's cmstat program
The program cmstat that is installed as part of the Infernal package
with Ribovore installation can be used to output information on the
model or models in CM file. For example, below is the output of
cmstat on the ribotyper.cm file:
> $RIBOINFERNALDIR/cmstat $RIBOINSTALLDIR/models/ribotyper.cm
# cmstat :: display summary statistics for CMs
# INFERNAL 1.1.4 (Dec 2020)
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# rel entropy
# ------------
# idx name accession nseq eff_nseq clen W bps bifs model cm hmm
# ---- ------------------------------------- --------- -------- -------- ----- ----- ---- ---- ----- ----- -----
1 SSU_rRNA_archaea RF01959 86 86.00 1477 2998 457 30 cm 1.496 1.315
2 SSU_rRNA_bacteria RF00177 99 99.00 1533 1866 462 31 cm 1.415 1.231
3 SSU_rRNA_eukarya RF01960 91 91.00 1851 2879 447 30 cm 1.004 0.888
4 SSU_rRNA_microsporidia RF02542 46 46.00 1312 1974 366 26 cm 1.231 1.083
5 SSU_rRNA_chloroplast - 94 94.00 1488 2288 446 31 cm 1.602 1.514
6 SSU_rRNA_mitochondria_metazoa - 83 83.00 954 1406 254 20 cm 1.089 0.971
7 SSU_rRNA_cyanobacteria - 49 49.00 1487 1576 445 31 cm 1.748 1.668
8 LSU_rRNA_archaea RF02540 91 91.00 2990 6270 786 68 cm 1.323 1.133
9 LSU_rRNA_bacteria RF02541 102 102.00 2925 5920 846 70 cm 1.352 1.153
10 LSU_rRNA_eukarya RF02543 88 88.00 3401 8019 872 71 cm 1.122 0.994
11 SSU_rRNA_apicoplast - 3 3.00 1463 1685 398 28 cm 0.926 0.721
12 SSU_rRNA_chloroplast_pilostyles - 1 1.00 1531 1557 440 30 cm 0.656 0.399
13 SSU_rRNA_mitochondria_amoeba - 2 2.00 1861 2004 311 25 cm 0.725 0.593
14 SSU_rRNA_mitochondria_chlorophyta - 2 2.00 1200 1549 224 19 cm 0.674 0.509
15 SSU_rRNA_mitochondria_fungi - 4 4.00 1603 2455 334 26 cm 0.908 0.764
16 SSU_rRNA_mitochondria_kinetoplast - 3 3.00 624 652 68 5 cm 0.978 0.910
17 SSU_rRNA_mitochondria_plant - 4 4.00 1951 2211 446 29 cm 1.353 1.256
18 SSU_rRNA_mitochondria_protist - 2 2.00 1677 2051 318 24 cm 0.732 0.582
For more information on cmstat see the Infernal user's guide
Cannone J.J., Subramanian S., Schnare M.N., Collett J.R., D'Souza L.M., Du Y., Feng B., Lin N., Madabusi L.V., MÜller K.M., Pande N., Shang Z., Yu N., and Gutell R.R. (2002). The Comparative RNA Web (CRW) Site: An Online Database of Comparative Sequence and Structure Information for Ribosomal, Intron, and Other RNAs. BioMed Central Bioinformatics, 3:2. [Correction: BioMed Central Bioinformatics. 3:15.]