Table 1

Forty-two pathogens included in PHIDIAS
Pathogens (disease)
 CDC/NIAID category
 No. of genomes
 Phinfo
 Pacodom
 Phinet
1
 Bacillus anthracis (anthrax)
 A/A
 3
 √
 4,588
 √
2
 Brucella spp. (brucellosis)
 B/B
 4
 √
 4,267
 √
3
 Burkholderia mallei (glanders)
 B/B
 1
 √
 4,679
 √
4
 Burkholderia pseudomallei (Melioidosis)
 B/B
 2
 √
 5,093
5
 Campylobacter jejuni (food safety threat)
 /B
 2
3,235
6
 Clostridium botulinum (botulism)
 A/A
 0
 √
 N/A
 √
7
 Clostridium perfringens (epsilon toxin)
 B/B
 1
3,770
8
 Coxiella burnetii (Q fever)
 B/B
 1
 √
 3,032
 √
9
 Escherichia coli (food safety threat)
 B/B
 6
 √
 5,440
 √
10
 Francisella tularensis (tularemia)
 A/A
 2
 √
 3,057
 √
11
 Helicobacter spp. (gastric ulcer)
5
3,374
12
 Legionella pneumophila (legionnaires' disease)
3
3,974
13
 Listeria monocytogenes (food safety threat)
 /B
 2
3,999
14
 Mycobacterium tuberculosis (tuberculosis)
 /C
 2
 √
 3,991
15
 Rickettsia prowazekii (typhus fever)
 /C
 1
 √
 2,129
 √
16
 Rickettsia rickettsii (Rocky Mountain spotted fever)
 /C
 0
 √
 N/A
 √
17
 Salmonella enterica (food safety threat)
 B/B
 4
 √
 5,150
 √
18
 Shigella spp. (food safety threat)
 B/B
 5
 √
 5,211
 √
19
 Vibrio spp. (water safety threat)
 B/B
 5
5,449
20
 Yersinia pestis (plague)
 A/A
 5
 √
 4,828
 √
21
 Crimean-Congo hemorrhagic fever virus (tickborne hemorrhagic fever)
 C/C
 1
 √
 4
 √
22
 Eastern equine encephalitis virus (encephalitis)
 B/B
 0
 √
 N/A
 √
23
 Foot-and-mouth disease virus (foot-and-mouth disease)
7
 √
 3
24
 Guanarito virus (viral hemorrhagic fever)
 A/A
 1
 √
 0
 √
25
 Human immunodeficiency virus (AIDS)
2
 √
 8
26
 Junin virus (viral hemorrhagic fever)
 A/A
 1
 √
 0
 √
27
 Lassa virus (viral hemorrhagic fever)
 A/A
 1
 √
 0
 √
28
 Louping ill virus (encephalomyelitis)
1
 √
 6
 √
29
 Machupo virus (viral hemorrhagic fever)
 A/A
 1
 √
 0
 √
30
 Marburg virus (viral hemorrhagic fever)
 A/A
 1
 √
 N/A
 √
31
 Measles virus (measles)
1
 √
 0
 √
32
 Newcastle Disease Virus (Newcastle disease)
0
 √
 N/A
33
 Powassan virus (encephalitis)
0
 √
 N/A
 √
34
 Reston ebola virus (viral hemorrhagic fever)
 A/A
 1
 √
 1
 √
35
 Rift Valley fever virus (Rift Valley fever)
 /A
 1
 √
 3
 √
36
 Variola virus (smallpox)
 A/A
 2
 √
 129
37
 Venezuelan equine encephalitis virus (viral encephalitis)
 B/B
 1
 √
 8
 √
38
 Yellow fever virus (yellow fever)
 /C
 1
 √
 5
 √
39
 Cryptosporidium parvum (cryptosporidiosis)
 B/B
 0
 √
 N/A
40
 Coccidioides immitis (meningitis)
0
 √
 N/A
41
 Phakopsora pachyrhizi (soybean rust)
0
 √
 N/A
 √
42
 Plasmodium falciparum (malaria)
0
 √
 N/A

Total (42 pathogens)
77
 37
 75,433
 27

The program includes 20 bacteria (54 genomes), 18 viruses (23 genomes), and 4 parasites. The database contains 75,433 conserved domains (7,919 unique PSSMs) and PHI network information for 27 pathogens.

Xiang et al. Genome Biology 2007 8:R150   doi:10.1186/gb-2007-8-7-r150

Open Data