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Table 1 Summary of genomes in the reference sets

From: Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment

 

Bacteria

 

Eukaryotes

 

Profile Architecture

Actino

Firmicutes

Spirochaetes

Proteo

Others

Archaea

Metazoans

Fungi

Plants

Apicomplexa

Others

Number of Genomes

B

3

10

2

17

9

0

0

0

0

0

0

41

BA

3

10

2

17

9

11

0

0

0

0

0

52

BAE1

3

10

2

17

9

11

0

1

1

1

0

55

BAE2

3

10

2

17

9

11

2

1

1

1

0

57

BAE3a

3

10

2

17

9

11

3

2

1

1

1

60

BAE3b

3

10

2

17

9

11

3

2

1

1

1

60

NR

2

9

2

14

7

11

3

2

1

1

1

53

NR-3

1

9

2

12

7

11

3

2

1

1

1

50

NR-8

1

8

2

10

6

10

3

2

1

1

1

45

LA

1

5

2

10

6

10

3

2

1

1

1

42

LAc

2

5

0

7

3

10

3

2

1

1

1

35

BAE4

3

10

2

17

9

11

19

16

1

5

2

95

BAE5

1

1

1

1

3

11

19

16

1

5

2

61

BAE6

1

2

1

3

5

3

2

2

1

1

2

23

AE

0

0

0

0

0

11

19

16

1

5

2

54

E

0

0

0

0

0

0

19

16

1

5

2

43

  1. Notes: B – All 41 bacterial genomes; BA – 41 bacterial and 11 archaeal genomes; BAE1 – BA genomes plus 3 eukaryotic genomes (S. cerevisiae, A. thaliana, P. falciparum); BAE2 – BA genomes plus 5 eukaryotic genomes (D. melanogaster, C. elegans, S. cerevisiae, A. thaliana, and P. falciparum); BAE3a – BA genomes plus 8 eukaryotic genomes (M. musculus, D. melanogaster, C. elegans, S. cerevisiae, S. pombe, D. discoideum, A. thaliana, and P. falcifarum); BAE3b – BA genomes plus 8 eukaryotic genomes (C. familiaris, A. mellifera, C. elegans, C. albicans, S. pombe, D. discoideum, A. thaliana, and P. vivax); NR – BAE3a minus 7 bacterial strains; NR-3 – NR minus 3 bacterial genomes (M. leprae, R. prowazekii, and X. fastidiosa); NR-8 – NR-3 minus 4 bacterial genomes (M. pulmonis, C. trachomatis, Buchnera sp. APS, and P. multocida) and 1 archaeal genome (P. abyssi); LA – NR-8 minus 3 bacterial genomes (S. pyogenes SF370, M. genitalium, and M. pneumoniae); LAc – Set of eukaryotic and archaeal genomes used in LA along with the set of bacterial genomes not included (complementary set) in LA; BAE4 – All 95 genomes under consideration (41 bacteria, 11 archaea, and 43 eukaryotes); BAE5 – All Archaeal and eukaryotic genomes plus a selected set of 7 bacterial genomes; BAE6 – A selected of 23 genomes (12 bacteria, 3 Archaea, and 8 eukaryotes); AE – All Archaeal and eukaryotic genomes; E – All 43 eukaryotic genomes.
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BMC Bioinformatics

ISSN: 1471-2105

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