Model overview
PhenDB uses Support Vector Machine (SVM) models for the prediction of traits. Below is a list of all models (click model name for further information). For each model, the maximal mean balanced accuracy (given a 100% complete, 0% contaminated metagenomic bin) is given.
Legend: T = from text mining E = from expert opinion M = inferred from marker gene presence C = from Feldbauer et al 2015
Model name | Description | Training date | Maximal accuracy |
---|---|---|---|
ARCHAEA | Organism is an archaeon (C) | 2018-06-19 08:50:24 | |
PEN_180 | Organism is resistant to penicillin (trained on S. aureus) (E) | 2018-06-19 08:55:24 | |
THERM | Organism has a thermophilic lifestyle (C) | 2018-06-19 08:58:05 | |
THERM_OR_TOLERANT | Organism has a thermophilic lifestyle or is thermotolerant (C) | 2018-06-19 08:58:27 | |
Aerobe | Organism is capable of aerobic respiration (T) | 2018-06-19 08:59:19 | |
Anaerobe | Organism is capable of anaerobic respiration (T) | 2018-06-19 08:59:52 | |
gram_stain | Cells of organism stain Gram-positive (+) or Gram-negative (-) (T) | 2018-06-19 09:00:19 | |
motility | Organism is capable of self-propelled motion (T) | 2018-06-19 09:00:54 | |
sporulation | Organism is capable of producing endospores for persistence (T) | 2018-06-19 09:01:24 | |
Sulfate_reducer | Organism is capable of using sulfate as terminal electron acceptor (T) | 2018-06-19 09:01:56 | |
amikacin_resistant | Organism is resistant to amikacin. (Trained on Acinetobacter baumannii.) (E) | 2018-09-11 09:32:47 | |
ciprofloxacin_resistant | Organism is resistant to ciprofloxacin. (Trained on Acinetobacter baumannii.) (E) | 2018-09-11 09:32:49 | |
alkb | Organism is capable of degrading alkanes (M) | 2019-02-01 14:12:13 | |
AOB | Organism is part of the clade of ammonia-oxidizing bacteria (E) | 2019-02-01 14:12:28 | |
ars | Organism is capable of arsenic detoxification (M) | 2019-02-01 14:12:36 | |
avre | Organism is a plant pathogen (based on AvrE virulence factor) (M) | 2019-02-01 14:12:49 | |
baicd | Organism is capable of producing secondary bile acids (M) | 2019-02-01 14:12:54 | |
bena | Organism is capable of degrading benzoate via hydroxylation (M) | 2019-02-01 14:13:02 | |
bpp | Organism is capable of hydrolyzing phytate (M) | 2019-02-01 14:13:21 | |
bsh | Organism is capable of deconjugating glycine and taurine from bile salts (M) | 2019-02-01 14:13:29 | |
buk2 | Organism is capable of producing butyrate (M) | 2019-02-01 14:13:37 | |
chb | Organism is capable of degrading chitine (M) | 2019-02-01 14:13:59 | |
cnta | Organism is capable of aromatic ring hydroxylation (M) | 2019-02-01 14:14:07 | |
coos | Organism is capable of assimilating CO (M) | 2019-02-01 14:14:12 | |
cutc | Organism is capable of producing trimethylamine via choline (M) | 2019-02-01 14:14:28 | |
dbfa4 | Organism is capable of performing dibenzofuran degradation (M) | 2019-02-01 14:14:38 | |
FACULTATIVE | Organism is a facultative anaerobe (C) | 2019-02-01 14:14:59 | |
HALO | Organism has a halophilic lifestyle (C) | 2019-02-01 14:15:25 | |
hsdh | Organism is capable of degrading bile acids (M) | 2019-02-01 14:15:40 | |
hyda | Organism is capable of producing H2 gas (M) | 2019-02-01 14:15:49 | |
METHANOTROPH | Organism is capable of growth with methane as the sole carbon source (C) | 2019-02-01 14:16:08 | |
naph2 | Organism is capable of degrading naphtalene (M) | 2019-02-01 14:16:25 | |
nif | Organism is capable of fixing N2 (E) | 2019-02-01 14:16:31 | |
NOB | Organism is part of the clade of nitrite-oxidizing bacteria (E) | 2019-02-01 14:16:53 | |
p450 | Organism is capable of degrading fatty acids (M) | 2019-02-01 14:16:59 | |
phnx | Organism is capable of hydrolyzing phosphonate (M) | 2019-02-01 14:17:19 | |
phod | Organism is capable of recycling organic phosphorus (M) | 2019-02-01 14:17:45 | |
PHOTO | Organism is capable of photon capture for energy acquisition (C) | 2019-02-01 14:18:05 | |
psa | Organism is capable of synthesizing capsular polysaccharide (M) | 2019-02-01 14:18:23 | |
PSYCHRO | Organism has a psychrophilic lifestyle (C) | 2019-02-01 14:18:28 | |
soxb | Organism is capable of oxidizing thiosulfate (M) | 2019-02-01 14:18:55 | |
SYMBIONT | Organism has an obligate intracellular lifestyle (C) | 2019-02-01 14:19:08 | |
T3SS | Organism expresses a Type III secretion system (C) | 2019-02-01 14:19:22 | |
T4SS | Organism expresses a Type IV secretion system (C) | 2019-02-01 14:19:48 | |
T6SS | Organism expresses a Type VI secretion system (C) | 2019-02-01 14:20:09 | |
txta | Organism is a plant pathogen (based on thaxtomin synthesis capability) (M) | 2019-02-01 14:20:35 | |
urea | Organism is capable of degrading urea (M) | 2019-02-01 14:20:49 | |
xen | Organism is capable of reducing various alpha-beta-unsaturated and nitro compounds (M) | 2019-02-01 14:21:02 | |
AUTO | Organism is capable of growth with CO2 as sole carbon source (C) | 2019-02-01 14:21:46 |