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ROCker

Accurately detecting functional genes in metagenomes

The following models are also available at GitHub: lmrodriguezr/rocker.

§ Index

AmoA: Ammonia monooxygenase
AmoA_B_v2 (bacterial, v2.0)
1 model: 125bp
Prepared by: Luis (Coto) Orellana
Comments: Explicitly excludes non-bacterial variants
Last update: Apr-18-2017
AmoA_A_v2 (archaeal, v2.0)
1 model: 125bp
Prepared by: Luis (Coto) Orellana
Comments: Explicitly excludes non-archaeal variants
Last update: Apr-18-2017
AmoA_B (bacterial)
6 models: 80bp, 100bp, 125bp, 150bp, 200bp, 250bp
Prepared by: Luis (Coto) Orellana
Comments: Explicitly excludes non-bacterial variants
Last update: Nov-06-2015
AmoA_A (archaeal)
1 model: 125bp
Prepared by: Luis (Coto) Orellana
Comments: Explicitly excludes non-archaeal variants
Last update: Nov-13-2015
BLA: Beta-lactamase
BlaA
2 models: 150bp, 250bp
Prepared by: Siyu Zhang
Comments: Class A beta-lactamase [with --search diamond]
Last update: Apr-19-2020
MBL
2 models: 150bp, 250bp
Prepared by: Brittany Suttner
Comments: Metalo-beta-lactamase (class B) [with --search diamond]
Last update: Feb-18-2020
MBL_S1_S2
2 models: 150bp, 250bp
Prepared by: Brittany Suttner
Comments: Metalo-beta-lactamase (class B) subclasses S1 and S2 [with --search diamond]
Last update: Feb-18-2020
MBL_S3
2 models: 150bp, 250bp
Prepared by: Brittany Suttner
Comments: Metalo-beta-lactamase (class B) subclass S3 [with --search diamond]
Last update: Feb-18-2020
BlaC
2 models: 150bp, 250bp
Prepared by: Siyu Zhang
Comments: Class C beta-lactamase
Last update: Feb-24-2020
OXA
2 models: 150bp, 250bp
Prepared by: Brittany Suttner
Comments: Beta-lactamase OXA family (blaOXA, class D) [with --search diamond]
Last update: Feb-18-2020
TEM
2 models: 150bp, 250bp
Prepared by: Siyu Zhang
Comments: Beta-lactamase TEM family (blaTEM) [with --search diamond]
Last update: Feb-24-2020
Hao: Hydroxylamine oxidoreductase
Hao
1 model: 125bp
Prepared by: Luis (Coto) Orellana
Last update: Apr-18-2017
KSalpha: Ketosynthase alpha subunit
KSalpha
1 model: 150bp
Prepared by: Brittany Suttner
Comments: Polyketide antibiotic biosynthesis
Last update: Nov-20-2018
NarG: Nitrate reductase
NarG
6 models: 80bp, 100bp, 150bp, 200bp, 250bp, 500bp
Prepared by: Despina Tsementzi & Luis M Rodriguez
Comments: [with --search diamond]
Last update: Jun-11-2015
NarG_NxrA: Nitrate reductase and nitrite oxidoreductase alpha subunit
NarG_NxrA
1 model: 125bp
Prepared by: Luis (Coto) Orellana
Last update: Apr-18-2017
NifH: Nitrogenase reductase subunit
NifH
3 models: 100bp, 150bp, 200bp
Prepared by: Luis M Rodriguez-R and John Christian Gaby
Last update: Aug-04-2018
NirK: Nitrite reductase
NirK
6 models: 80bp, 100bp, 150bp, 200bp, 250bp, 500bp
Prepared by: Luis (Coto) Orellana
Last update: Jul-14-2015
NirK_cladeThau (clade Thaumarchaeota)
1 model: 125bp
Prepared by: Luis (Coto) Orellana
Last update: Apr-18-2017
NirK_cladeIII (clade III)
1 model: 125bp
Prepared by: Luis (Coto) Orellana
Last update: Apr-18-2017
NirK_cladeI-II (clades I and II)
1 model: 125bp
Prepared by: Luis (Coto) Orellana
Last update: Apr-18-2017
NorB: Nitric oxide reductase
NorB
1 model: 125bp
Prepared by: Luis (Coto) Orellana
Last update: Apr-18-2017
NosZ: Nitrous oxide reductase
NosZ
7 models: 80bp, 100bp, 125bp, 150bp, 200bp, 250bp, 500bp
Prepared by: Luis (Coto) Orellana
Last update: Jul-14-2015
NosZ_v2 (v2.0)
1 model: 125bp
Prepared by: Luis (Coto) Orellana
Last update: Apr-18-2017
NrfA: Nitrite reductase, formate-dependent
NrfA
1 model: 125bp
Prepared by: Luis (Coto) Orellana
Last update: Apr-18-2017
OxyT: N,N-dimethyltransferase
OxyT
1 model: 150bp
Prepared by: Brittany Suttner
Comments: Tetracycline biosynthesis
Last update: Apr-13-2018
RpoB: Ribosomal RNA polymerase B subunit
RpoB
6 models: 80bp, 100bp, 150bp, 200bp, 250bp, 500bp
Prepared by: Luis M Rodriguez-R
Comments: [with --search diamond]
Last update: Jun-09-2015
TetM: Tetracycline resistance
TetM
2 models: 100bp, 150bp
Prepared by: Brittany Suttner
Last update: Apr-10-2018
UreC: Urease subunit alpha
UreC
1 model: 125bp
Prepared by: Luis (Coto) Orellana
Last update: Apr-18-2017


§ Models

FNR: False Negative Rate (1-Sensitivity), FPR: False Positive Rate or fall-out (1-Specificity), Acc: Accuracy.

Model Name Length Statistics ROCker Plot ROCker model Training Set Comments
AmoA: Ammonia monooxygenase
AmoA_B_v2125bpFNR: 7.4%
FPR: 0.36%
Acc: 98.1%		ROCker plot of AmoA_B_v2Download
Search online		Positive:
8 proteins
Negative:
14 proteins
Reference sequences		Explicitly excludes non-bacterial variants
Last update: Apr-18-2017
AmoA_A_v2125bp-ROCker plot of AmoA_A_v2Download
Search online		Positive:
5 proteins
Negative:
16 proteins
Reference sequences		Explicitly excludes non-archaeal variants
Last update: Apr-18-2017
AmoA_B80bp-ROCker plot of AmoA_BDownload
Search online		Positive:
7 proteins
Negative:
14 proteins
Reference sequences		Explicitly excludes non-bacterial variants
Last update: Nov-06-2015
100bp-ROCker plot of AmoA_BDownload
Search online
125bp-ROCker plot of AmoA_BDownload
Search online
150bp-ROCker plot of AmoA_BDownload
Search online
200bp-ROCker plot of AmoA_BDownload
Search online
250bp-ROCker plot of AmoA_BDownload
Search online
AmoA_A125bp-ROCker plot of AmoA_ADownload
Search online		Positive:
5 proteins
Negative:
16 proteins
Reference sequences		Explicitly excludes non-archaeal variants
Last update: Nov-13-2015
BLA: Beta-lactamase
BlaA150bpFNR: 1.9422%
FPR: 0.0055%
Acc: 99.982%		ROCker plot of BlaADownload
Search online		Positive:
353 proteins
Negative:
84 proteins
Reference sequences (Trimmed)		Class A beta-lactamase
[with --search diamond]
Last update: Apr-19-2020
250bpFNR: 2.5372%
FPR: 0.0042%
Acc: 99.987%		ROCker plot of BlaADownload
Search online
MBL150bpFNR: 2.71%
FPR: 0.045%
Acc: 99.8%		ROCker plot of MBLDownload
Search online		Positive:
86 proteins
Negative:
5 proteins
Reference sequences (Trimmed)		Metalo-beta-lactamase (class B)
[with --search diamond]
Last update: Feb-18-2020
250bpFNR: 2.51%
FPR: 0.045%
Acc: 99.9%		ROCker plot of MBLDownload
Search online
MBL_S1_S2150bpFNR: 1.01%
FPR: 0.17%
Acc: 99.7%		ROCker plot of MBL_S1_S2Download
Search online		Positive:
65 proteins
Negative:
5 proteins
Reference sequences (Trimmed)		Metalo-beta-lactamase (class B) subclasses S1 and S2
[with --search diamond]
Last update: Feb-18-2020
250bpFNR: 0.631%
FPR: 0.0897%
Acc: 99.9%		ROCker plot of MBL_S1_S2Download
Search online
MBL_S3150bpFNR: 5.72%
FPR: 0.237%
Acc: 99.6%		ROCker plot of MBL_S3Download
Search online		Positive:
71 proteins
Negative:
5 proteins
Reference sequences (Trimmed)		Metalo-beta-lactamase (class B) subclass S3
[with --search diamond]
Last update: Feb-18-2020
250bpFNR: 3.44%
FPR: 2.87%
Acc: 97.1%		ROCker plot of MBL_S3Download
Search online
BlaC150bpFNR: 1.864%
FPR: 9.0E-5%
Acc: 99.999%		ROCker plot of BlaCDownload
Search online		Positive:
152 proteins
Negative:
44 proteins
Reference sequences (Trimmed)		Class C beta-lactamase
Last update: Feb-24-2020
250bpFNR: 2.166%
FPR: 0.00022%
Acc: 99.999%		ROCker plot of BlaCDownload
Search online
OXA150bpFNR: 0.878%
FPR: 0.174%
Acc: 99.8%		ROCker plot of OXADownload
Search online		Positive:
136 proteins
Negative:
30 proteins
Reference sequences (Trimmed)		Beta-lactamase OXA family (blaOXA, class D)
[with --search diamond]
Last update: Feb-18-2020
250bpFNR: 2.58%
FPR: 0.0898%
Acc: 99.9%		ROCker plot of OXADownload
Search online
TEM150bpFNR: 1.186%
FPR: 0.818%
Acc: 98.98%		ROCker plot of TEMDownload
Search online		Positive:
11 proteins
Negative:
33 proteins
Reference sequences (Trimmed)		Beta-lactamase TEM family (blaTEM)
[with --search diamond]
Last update: Feb-24-2020
250bpFNR: 3.524%
FPR: 0.722%
Acc: 97.89%		ROCker plot of TEMDownload
Search online
Hao: Hydroxylamine oxidoreductase
Hao125bpFNR: 1.28%
FPR: 0.11%
Acc: 99.14%		ROCker plot of HaoDownload
Search online		Positive:
23 proteins
Negative:
9 proteins
Reference sequences		Last update: Apr-18-2017
KSalpha: Ketosynthase alpha subunit
KSalpha150bp-ROCker plot of KSalphaDownload
Search online		Positive:
26 proteins
Reference sequences		Polyketide antibiotic biosynthesis
Last update: Nov-20-2018
NarG: Nitrate reductase
NarG80bpFNR: 0.1%
FPR: 11.41%
Acc: 97.81%		ROCker plot of NarGDownload
Search online		Positive:
679 proteins
Negative:
31 proteins
Reference sequences
[with --search diamond]
Last update: Jun-11-2015
100bpFNR: 0.98%
FPR: 5.3%
Acc: 97.58%		ROCker plot of NarGDownload
Search online
150bpFNR: 0.27%
FPR: 0.2%
Acc: 99.8%		ROCker plot of NarGDownload
Search online
200bpFNR: 0.24%
FPR: 0.12%
Acc: 99.87%		ROCker plot of NarGDownload
Search online
250bpFNR: 0.39%
FPR: 0.09%
Acc: 99.91%		ROCker plot of NarGDownload
Search online
500bpFNR: 0.49%
FPR: 0.04%
Acc: 99.95%		ROCker plot of NarGDownload
Search online
NarG_NxrA: Nitrate reductase and nitrite oxidoreductase alpha subunit
NarG_NxrA125bp-ROCker plot of NarG_NxrADownload
Search online		Positive:
305 proteins
Reference sequences		Last update: Apr-18-2017
NifH: Nitrogenase reductase subunit
NifH100bpFNR: 21.7%
FPR: 0.0045%
Acc: 99.98%		ROCker plot of NifHDownload
Search online		Positive:
120 proteins
Negative:
56 proteins
Reference sequences		Last update: Aug-04-2018
150bpFNR: 23.09%
FPR: 0.0031%
Acc: 99.98%		ROCker plot of NifHDownload
Search online
200bpFNR: 27.1%
FPR: 0.0036%
Acc: 99.98%		ROCker plot of NifHDownload
Search online
NirK: Nitrite reductase
NirK80bpFNR: 1.99%
FPR: 2.72%
Acc: 97.82%		ROCker plot of NirKDownload
Search online		Positive:
147 proteins
Reference sequences		Last update: Jul-14-2015
100bpFNR: 2.76%
FPR: 1.49%
Acc: 97.71%		ROCker plot of NirKDownload
Search online
150bpFNR: 2.17%
FPR: 0.73%
Acc: 98.63%		ROCker plot of NirKDownload
Search online
200bpFNR: 1.72%
FPR: 0.57%
Acc: 99.02%		ROCker plot of NirKDownload
Search online
250bpFNR: 1.93%
FPR: 0.49%
Acc: 99.06%		ROCker plot of NirKDownload
Search online
500bpFNR: 1.64%
FPR: 0.68%
Acc: 99.04%		ROCker plot of NirKDownload
Search online
NirK_cladeThau125bp-ROCker plot of NirK_cladeThauDownload
Search online		Positive:
18 proteins
Reference sequences		Last update: Apr-18-2017
NirK_cladeIII125bp-ROCker plot of NirK_cladeIIIDownload
Search online		Positive:
10 proteins
Reference sequences		Last update: Apr-18-2017
NirK_cladeI-II125bp-ROCker plot of NirK_cladeI-IIDownload
Search online		Positive:
134 proteins
Negative:
8 proteins
Reference sequences		Last update: Apr-18-2017
NorB: Nitric oxide reductase
NorB125bp-ROCker plot of NorBDownload
Search online		Positive:
304 proteins
Reference sequences		Last update: Apr-18-2017
NosZ: Nitrous oxide reductase
NosZ80bpFNR: 0.89%
FPR: 7.44%
Acc: 98.65%		ROCker plot of NosZDownload
Search online		Positive:
173 proteins
Reference sequences		Last update: Jul-14-2015
100bpFNR: 1.09%
FPR: 5.44%
Acc: 98.33%		ROCker plot of NosZDownload
Search online
125bpFNR: 1.09%
FPR: 0.66%
Acc: 99.01%		ROCker plot of NosZDownload
Search online
150bpFNR: 0.73%
FPR: 1.82%
Acc: 98.94%		ROCker plot of NosZDownload
Search online
200bpFNR: 1.16%
FPR: 0.84%
Acc: 98.97%		ROCker plot of NosZDownload
Search online
250bpFNR: 0.61%
FPR: 0.75%
Acc: 99.33%		ROCker plot of NosZDownload
Search online
500bpFNR: 0.73%
FPR: 0.24%
Acc: 99.51%		ROCker plot of NosZDownload
Search online
NosZ_v2125bp-ROCker plot of NosZ_v2Download
Search online		Positive:
167 proteins
Reference sequences		Last update: Apr-18-2017
NrfA: Nitrite reductase, formate-dependent
NrfA125bp-ROCker plot of NrfADownload
Search online		Positive:
260 proteins
Negative:
8 proteins
Reference sequences		Last update: Apr-18-2017
OxyT: N,N-dimethyltransferase
OxyT150bp-ROCker plot of OxyTDownload
Search online		Positive:
10 proteins
Negative:
4 proteins
Reference sequences		Tetracycline biosynthesis
Last update: Apr-13-2018
RpoB: Ribosomal RNA polymerase B subunit
RpoB80bpFNR: 0.05%
FPR: 0.64%
Acc: 99.9%		ROCker plot of RpoBDownload
Search online		Positive:
757 proteins
Reference sequences
[with --search diamond]
Last update: Jun-09-2015
100bpFNR: 0.1%
FPR: 0.59%
Acc: 99.81%		ROCker plot of RpoBDownload
Search online
150bpFNR: 0.13%
FPR: 0.01%
Acc: 99.98%		ROCker plot of RpoBDownload
Search online
200bpFNR: 0.22%
FPR: 0.01%
Acc: 99.98%		ROCker plot of RpoBDownload
Search online
250bpFNR: 0.17%
FPR: 0%
Acc: 99.99%		ROCker plot of RpoBDownload
Search online
500bpFNR: 0.29%
FPR: 0%
Acc: 99.99%		ROCker plot of RpoBDownload
Search online
TetM: Tetracycline resistance
TetM100bp-ROCker plot of TetMDownload
Search online		Positive:
60 proteins
Negative:
4 proteins
Reference sequences		Last update: Apr-10-2018
150bp-ROCker plot of TetMDownload
Search online
UreC: Urease subunit alpha
UreC125bpFNR: 0.58%
FPR: 0.01%
Acc: 99.98%		ROCker plot of UreCDownload
Search online		Positive:
103 proteins
Reference sequences		Last update: Apr-18-2017