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Table 2 Percentage of genes detected using sequence alignment.

From: Gene function prediction based on genomic context clustering and discriminative learning: an application to bacteriophages

Reference Genome

 

Terminase

Portal

Head

Tail

Tape measure

Prohead protease

Lysin

Holin

Integrase

 

E-value cutoff

0.01

0.1

0.01

0.1

0.01

0.1

0.01

0.1

0.01

0.1

0.01

0.1

0.01

0.1

0.01

0.1

0.01

0.1

Bacteriophage bIL285

 

31

37

33

50

-

-

4

19

-

-

46

49

16

18

11

23

57

64

Lactococcus phage TP901-1

 

8

22

13

19

12

27

7

22

96

98

-

-

30

48

13

13

3

15

Enterobacteria phage HK97

 

29

40

35

43

4

26

12

19

83

96

54

64

0

4

5

24

54

73

Bacteriophage phi LC3

 

19

42

9

25

14

24

4

25

63

83

-

-

36

48

13

14

58

65

Staphylococcus aureus phage phi 13

 

12

25

40

56

9

19

-

-

77

94

36

38

-

-

13

26

62

71

  1. The percentages are calculated by dividing the number of significantly similar sequences by the total number of sequences found by using regular expression. Sequence similarity is determined by BLAST (bl2seq) [33] using BLOSUM45 with indicated E-value cutoffs. Each sequence is "blasted" against its corresponding gene in the reference genome. The best cases are highlighted in bold.