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Table 2 The benchmarking results on the non-structural alignments of the CMfinder dataset ( β=10)

From: Incorporating phylogenetic-based covarying mutations into RNAalifold for RNA consensus structure prediction

Family

MPI

RNAalifold

PhyloRNAalifold

RNAalifold

with RIBOSUM

PhyloRNAalifold

with RIBOSUM

PETFold

Cobalamin

43.2

-0.001

-0.001

-0.002

-0.002

-0.002

ctRNA_pGA1

66.5

0.865

0.889

0.979

0.979

0.936

Entero_CRE

81.7

0.912

0.912

0.916

0.916

1.000

Entero_OriR

87.5

0.694

0.830

0.965

0.965

0.910

glmS

55.2

0.445

0.566

0.873

0.784

0.811

Histone3

45.1

1.000

1.000

1.000

1.000

1.000

Intron_gpII

46.2

0.760

0.794

0.826

0.826

0.794

IRE

77.3

0.480

0.480

0.710

0.710

0.816

let-7

66.7

0.760

0.761

0.666

0.666

0.742

lin-4

64.6

0.523

0.521

0.712

0.712

0.739

Lysine

44.0

0.307

0.414

0.513

0.484

0.388

mir-10

68.4

0.741

0.820

0.957

0.957

0.935

Purine

53.8

0.852

0.977

0.977

0.977

0.953

RFN

64.2

0.342

0.309

0.302

0.433

0.477

Rhino_CRE

81.4

0.581

0.581

0.976

0.976

0.750

S_box

56.5

0.430

0.430

0.817

0.860

0.750

s2m

78.3

1.000

1.000

1.000

1.000

1.000

SECIS

36.5

0.000

0.000

0.000

0.000

-0.003

Tymo_tRNA-like

64.1

0.691

0.703

0.768

0.768

0.596

 

Mean

0.599

0.631

0.735

0.737

0.715

 

Specificity

0.947

0.947

0.947

0.947

0.999

 

Sensitivity

0.486

0.545

0.689

0.704

0.655

  1. The MCC on non-structural alignments of the CMfinder dataset is compared between PhyloRNAalifold, RNAalifold and PETfold. The parameter β of PhyloRNAalifold is 10. Best performance on the same family is set to bold.