ROCker

Accurately detecting functional genes in metagenomes

The following models are also available at GtiHub: lhor/rocker-models.


§ 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
Hao: Hydroxylamine oxidoreductase
Hao
1 model: 125bp
Prepared by: Luis (Coto) Orellana
Last update: Apr-18-2017
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
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
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 Files Training Set Comments
AmoA: Ammonia monooxygenase
AmoA_B_v2125bpFNR: 7.4
FPR: 0.36
Acc: 98.1
ROCker plot of AmoA_B_v2ROCker modelPositive:
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_v2ROCker modelPositive:
5 proteins
Negative:
16 proteins
Reference sequences
Explicitly excludes non-archaeal variants
Last update: Apr-18-2017
AmoA_B80bp-ROCker plot of AmoA_BROCker modelPositive:
7 proteins
Negative:
14 proteins
Reference sequences
Explicitly excludes non-bacterial variants
Last update: Nov-06-2015
100bp-ROCker plot of AmoA_BROCker model
125bp-ROCker plot of AmoA_BROCker model
150bp-ROCker plot of AmoA_BROCker model
200bp-ROCker plot of AmoA_BROCker model
250bp-ROCker plot of AmoA_BROCker model
AmoA_A125bp-ROCker plot of AmoA_AROCker modelPositive:
5 proteins
Negative:
16 proteins
Reference sequences
Explicitly excludes non-archaeal variants
Last update: Nov-13-2015
Hao: Hydroxylamine oxidoreductase
Hao125bpFNR: 1.28
FPR: 0.11
Acc: 99.14
ROCker plot of HaoROCker modelPositive:
23 proteins
Negative:
9 proteins
Reference sequences
Last update: Apr-18-2017
NarG: Nitrate reductase
NarG80bpFNR: 0.1
FPR: 11.41
Acc: 97.81
ROCker plot of NarGROCker modelPositive:
679 proteins
Negative:
31 proteins
Reference sequences
Last update: Jun-11-2015
100bpFNR: 0.98
FPR: 5.3
Acc: 97.58
ROCker plot of NarGROCker model
150bpFNR: 0.27
FPR: 0.2
Acc: 99.8
ROCker plot of NarGROCker model
200bpFNR: 0.24
FPR: 0.12
Acc: 99.87
ROCker plot of NarGROCker model
250bpFNR: 0.39
FPR: 0.09
Acc: 99.91
ROCker plot of NarGROCker model
500bpFNR: 0.49
FPR: 0.04
Acc: 99.95
ROCker plot of NarGROCker model
NarG_NxrA: Nitrate reductase and nitrite oxidoreductase alpha subunit
NarG_NxrA125bp-ROCker plot of NarG_NxrAROCker modelPositive:
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 NifHROCker modelPositive:
120 proteins
Negative:
56 proteins
Reference sequences
Last update: Aug-04-2018
150bpFNR: 23.09
FPR: 0.0031
Acc: 99.98
ROCker plot of NifHROCker model
200bpFNR: 27.1
FPR: 0.0036
Acc: 99.98
ROCker plot of NifHROCker model
NirK: Nitrite reductase
NirK80bpFNR: 1.99
FPR: 2.72
Acc: 97.82
ROCker plot of NirKROCker modelPositive:
147 proteins
Reference sequences
Last update: Jul-14-2015
100bpFNR: 2.76
FPR: 1.49
Acc: 97.71
ROCker plot of NirKROCker model
150bpFNR: 2.17
FPR: 0.73
Acc: 98.63
ROCker plot of NirKROCker model
200bpFNR: 1.72
FPR: 0.57
Acc: 99.02
ROCker plot of NirKROCker model
250bpFNR: 1.93
FPR: 0.49
Acc: 99.06
ROCker plot of NirKROCker model
500bpFNR: 1.64
FPR: 0.68
Acc: 99.04
ROCker plot of NirKROCker model
NirK_cladeThau125bp-ROCker plot of NirK_cladeThauROCker modelPositive:
18 proteins
Reference sequences
Last update: Apr-18-2017
NirK_cladeIII125bp-ROCker plot of NirK_cladeIIIROCker modelPositive:
10 proteins
Reference sequences
Last update: Apr-18-2017
NirK_cladeI-II125bp-ROCker plot of NirK_cladeI-IIROCker modelPositive:
134 proteins
Negative:
8 proteins
Reference sequences
Last update: Apr-18-2017
NorB: Nitric oxide reductase
NorB125bp-ROCker plot of NorBROCker modelPositive:
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 NosZROCker modelPositive:
173 proteins
Reference sequences
Last update: Jul-14-2015
100bpFNR: 1.09
FPR: 5.44
Acc: 98.33
ROCker plot of NosZROCker model
125bpFNR: 1.09
FPR: 0.66
Acc: 99.01
ROCker plot of NosZROCker model
150bpFNR: 0.73
FPR: 1.82
Acc: 98.94
ROCker plot of NosZROCker model
200bpFNR: 1.16
FPR: 0.84
Acc: 98.97
ROCker plot of NosZROCker model
250bpFNR: 0.61
FPR: 0.75
Acc: 99.33
ROCker plot of NosZROCker model
500bpFNR: 0.73
FPR: 0.24
Acc: 99.51
ROCker plot of NosZROCker model
NosZ_v2125bp-ROCker plot of NosZ_v2ROCker modelPositive:
167 proteins
Reference sequences
Last update: Apr-18-2017
NrfA: Nitrite reductase, formate-dependent
NrfA125bp-ROCker plot of NrfAROCker modelPositive:
260 proteins
Negative:
8 proteins
Reference sequences
Last update: Apr-18-2017
RpoB: Ribosomal RNA polymerase B subunit
RpoB80bpFNR: 0.05
FPR: 0.64
Acc: 99.9
ROCker plot of RpoBROCker modelPositive:
757 proteins
Reference sequences
Last update: Jun-09-2015
100bpFNR: 0.1
FPR: 0.59
Acc: 99.81
ROCker plot of RpoBROCker model
150bpFNR: 0.13
FPR: 0.01
Acc: 99.98
ROCker plot of RpoBROCker model
200bpFNR: 0.22
FPR: 0.01
Acc: 99.98
ROCker plot of RpoBROCker model
250bpFNR: 0.17
FPR: 0
Acc: 99.99
ROCker plot of RpoBROCker model
500bpFNR: 0.29
FPR: 0
Acc: 99.99
ROCker plot of RpoBROCker model
UreC: Urease subunit alpha
UreC125bpFNR: 0.58
FPR: 0.01
Acc: 99.98
ROCker plot of UreCROCker modelPositive:
103 proteins
Reference sequences
Last update: Apr-18-2017