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Table 1 Evaluation of RNAstrand.

From: RNAstrand: reading direction of structured RNAs in multiple sequence alignments

    

c = 0

  

c = 0.5

  

c = 0.9

  

ncRNA type

N a

N c

A

A +

A -

A

1-A-u

u

A

1-A-u

u

A(RNAz)

Alignments classified as structured RNA by RNAz

5S rRNA

413

1

0.990

0.993

0.988

0.978

0.006

0.016

0.958

0.000

0.042

0.973

5.8S rRNA

146

1

0.932

0.932

0.932

0.894

0.055

0.051

0.733

0.024

0.243

0.904

tRNA

286

1

0.948

0.948

0.948

0.886

0.017

0.096

0.621

0.009

0.371

0.535

miRNA

1875

43

0.981 [0.241]

0.979 [0.246]

0.982 [0.238]

0.965 [0.261]

0.009 [0.171]

0.026 [0.147]

0.906 [0.373]

0.001 [0.003]

0.094 [0.372]

0.187 [0.376]

snoRNA (C/D)

946

71

0.780 [0.376]

0.785 [0.374]

0.775 [0.389]

0.732 [0.411]

0.190 [0.363]

0.078 [0.256]

0.618 [0.431]

0.147 [0.286]

0.235 [0.416]

0.654 [0.446]

snoRNA (H/ACA)

3066

53

0.909 [0.198]

0.908 [0.198]

0.909 [0.199]

0.882 [0.255]

0.062 [0.160]

0.056 [0.184]

0.823 [0.352]

0.021 [0.039]

0.156 [0.339]

0.899 [0.283]

spliceos. RNA

896

6

0.877 [0.252]

0.885 [0.251]

0.868 [0.254]

0.831 [0.327]

0.086 [0.212]

0.083 [0.118]

0.735 [0.322]

0.042 [0.125]

0.222 [0.202]

0.835 [0.257]

euk. SRP RNA

891

1

0.997

0.998

0.996

0.992

0.001

0.007

0.972

0.000

0.028

0.841

nucl. RNaseP

31

1

0.694

0.710

0.677

0.613

0.274

0.113

0.387

0.081

0.532

0.290

RNase MRP

140

1

0.989

0.986

0.993

0.982

0.000

0.018

0.961

0.000

0.039

0.500

IRES

170

8

0.715 [0.453]

0.718 [0.455]

0.712 [0.452]

0.647 [0.469]

0.200 [0.424]

0.153 [0.339]

0.597 [0.448]

0.106 [0.433]

0.297 [0.402]

0.318 [0.424]

SECIS

76

1

0.651

0.658

0.645

0.520

0.257

0.224

0.329

0.191

0.480

0.487

7SK

184

1

0.041

0.043

0.038

0.024

0.916

0.060

0.011

0.802

0.188

0.038

Alignments not classified as structured RNA by RNAz

5S rRNA

525

1

0.793

0.821

0.766

0.717

0.130

0.153

0.552

0.057

0.390

-

5.8S rRNA

1000

1

0.853

0.892

0.814

0.771

0.092

0.137

0.602

0.032

0.366

-

tRNA

1

1

1/1

1/1

1/1

1/1

0/1

0/1

1/1

0/1

0/1

-

miRNA

0

-

-

-

-

-

-

-

-

-

-

-

snoRNA (C/D)

4228

105

0.563 [0.397]

0.595 [0.399]

0.532 [0.414]

0.480 [0.420]

0.353 [0.363]

0.167 [0.236]

0.340 [0.394]

0.245 [0.316]

0.415 [0.364]

-

snoRNA (H/ACA)

1993

36

0.788 [0.251]

0.812 [0.244]

0.763 [0.291]

0.735 [0.314]

0.157 [0.203]

0.108 [0.233]

0.644 [0.370]

0.081 [0.169]

0.274 [0.339]

-

spliceos. RNA

2944

4

0.632 [0.287]

0.669 [0.287]

0.595 [0.289]

0.560 [0.314]

0.301 [0.261]

0.139 [0.071]

0.422 [0.338]

0.203 [0.200]

0.375 [0.180]

-

euk. SRP RNA

3

1

3/3

3/3

3/3

3/3

0/3

0/3

3/3

0/3

0/3

-

nucl. RNaseP

2

1

2/2

2/2

2/2

2/2

0/2

0/2

1/2

0/2

1/2

-

RNase MRP

0

-

-

-

-

-

-

-

-

-

-

-

IRES

265

13

0.506 [0.454]

0.521 [0.454]

0.491 [0.454]

0.468 [0.411]

0.457 [0.450]

0.075 [0.276]

0.436 [0.401]

0.353 [0.411]

0.211 [0.418]

-

SECIS

43

1

0.686

0.698

0.674

0.593

0.174

0.233

0.302

0.070

0.628

-

7SK

630

1

0.127

0.152

0.102

0.063

0.798

0.139

0.018

0.640

0.342

-

  1. N a : number of alignments in test set, N c : number of different RNA classes, A: accuracy, which is defined as the fraction of correctly classified input alignments, A+: accuracy of alignments in reading direction of ncRNA, A-: accuracy of reverse complementary alignments, u: fraction of undecided alignments, 1 - A - u: fraction of misclassified alignments, A(RNAz): fraction of alignments correctly classified by taking the strand with the largest RNAz probability as the strand of the ncRNA. Standard deviations for RNA families with alignments from different classes are given in brackets. Note, that in case c = 0 no undecided alignments are observed.
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Algorithms for Molecular Biology

ISSN: 1748-7188