Method

Algorithm

Correct helix count

Correct helix locations

Correct Nterminal

FP helix

FN helix

Correct SP topology

Correct RE topology

Correct topology


MEMSATSVM

SVM

95%

91%

91%

4%

5%

93%

64%

89%

OCTOPUS

NN + HMM

86%

83%

84%

14%

2%

21%

73%

79%

MEMSAT3

NN

84%

76%

84%

8%

8%

57%

64%

76%

ENSEMBLE

NN + HMM

77%

76%

79%

18%

5%

7%

55%

67%

PHOBIUS

HMM

75%

76%

79%

9%

16%

93%

36%

63%

HMMTOP

HMM

77%

76%

78%

18%

6%

29%

64%

63%

PRODIV

HMM

79%

64%

76%

19%

8%

0%

18%

57%

SVMTOP

SVM

66%

64%

66%

22%

22%

0%

55%

53%

TMHMM

HMM

75%

68%

72%

14%

20%

29%

55%

53%

PHDhtm

NN

75%

54%

55%

23%

30%

29%

18%

45%

 Column 1: Method – Prediction method. Column 2: Algorithm – Underlying machinelearning algorithm. Column 3: Correct helix count – Fraction of sequences with the correct number of TM helices predicted. Column 4: Correct helix locations – Fraction of sequences with the correct number and locations of TM helices predicted. Column 5: Correct Nterminal – Fraction of sequences with the correct Nterminal location predicted. Column 6: FP helix – Fraction of sequences with at least one over predicted TM helix. Column 7: FN helix – Fraction of sequences with at least one under predicted TM helix. Column 8: Correct SP topology: Fraction of sequences that contain signal peptides that have correct overall topology predicted. Column 9: Correct RE topology: Fraction of sequences that contain reentrant helices that have correct overall topology predicted. Column 10: Correct topology: Fraction of sequences that have correct overall topology predicted, requiring the correct number and location of TM helices and correct location of the Nterminal. TM helices must overlap their defined positions by at least 5 residues.