MP4: a machine learning based classification tool for prediction and functional annotation of pathogenic proteins from metagenomic and genomic datasets

Gupta, Ankit; Malwe, Aditya S.; Srivastava, Gopal N.; Thoudam, Parikshit; Hibare, Keshav; Sharma, Vineet K.

doi:10.1186/s12859-022-05061-7

Table 7 Performance validation of MP4 on pathogenic protein dataset

From: MP4: a machine learning based classification tool for prediction and functional annotation of pathogenic proteins from metagenomic and genomic datasets

Strains	Class 1	Class 2	Class 3	Total sequences	Pathogenicity index	References
Bacillus anthracis A2012 uid54101	42	96	159	297	0.859	https://www.ncbi.nlm.nih.gov/bioproject?cmd=Retrieve&dopt=Overview&list_uids=299
Prevotella melaninogenica ATCC 25,845 uid51377	344	288	1661	2293	0.85	http://hmp.jcvi.org/jumpstart/hmp013/index.shtml
Chlamydophila psittaci 6BC uid63621	154	139	682	975	0.842	https://doi.org/10.1128/mBio.00604-12
Chlamydophila pneumoniae TW 183 uid57997	178	160	775	1113	0.84	PMID: 26420648
Helicobacter pylori B8 uid49873	314	197	1196	1707	0.816	PMID:21896079
Helicobacter pylori SouthAfrica20 uid216150	320	218	1164	1702	0.812	PMID: 21081026
Shigella dysenteriae 1617 uid229875	1224	2520	2665	6409	0.809
Providencia stuartii MRSN 2154 uid162193	900	920	2279	4099	0.78
Francisella tularensis holarctica F92 uid181998	407	600	835	1842	0.779	PMC3569339
Escherichia coli CFT073 uid57915	1196	1519	2649	5364	0.777	PMID: 12471157
Proteus mirabilis HI4320 uid61599	817	786	2059	3662	0.777	PMID: 18375554
Klebsiella pneumoniae 342 uid59145	1302	1649	2815	5766	0.774	https://doi.org/10.1371/journal.pgen.1000141
Capnocytophaga ochracea DSM 7271 uid59197	493	616	1062	2171	0.773	PMID: 21304645
Citrobacter koseri ATCC BAA 895 uid58143	1153	1397	2456	5006	0.77	PMID:12751719
Escherichia coli clone D i14 uid162049	1138	1342	2438	4918	0.769	https://doi.org/10.1371/journal.ppat.1006525
Mycoplasma pneumoniae 309 uid85495	164	107	436	707	0.768	PMID:18754792
Enterobacter aerogenes KCTC 2190 uid68103	1171	1330	2411	4912	0.762	PMID: 22493190
Shigella sonnei 53G uid84383	1303	1586	2521	5410	0.759	https://www.ncbi.nlm.nih.gov/genome/?term=Shigella+sonnei+53G+uid84383
Treponema pallidum DAL 1 uid87065	256	404	396	1056	0.758	PMID: 23449808
Enterobacter cloacae SCF1 uid59969	1067	1249	2083	4399	0.757	PMC3236048
Moraxella catarrhalis BBH18 uid48809	460	452	974	1886	0.756	PMID: 20453089
Capnocytophaga canimorsus Cc5 uid70727	590	607	1207	2404	0.755	https://doi.org/10.1371/journal.ppat.1000164
Shigella flexneri 2,002,017 uid159233	1160	1239	2304	4703	0.753	PMID: 19955273
Nocardia brasiliensis ATCC 700,358 uid86913	2081	3731	2602	8414	0.753	PMC3347167
Salmonella typhimurium DT104 uid223287	1159	1280	2153	4592	0.748	PMID: 9752592

Where, Class 1: Non-pathogenic proteins; Class 2: Antibiotic resistance and toxic proteins and Class 3: Secretory and capsular proteins

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