Table 2

Results on the RNA STRAND-Rfam dataset

RNA

comment

RIBOSUM

RNAalifold

Pfold

KNetFold

McC_mea


7SK

0.507

0.456

0.292

0.429

0.306

bicoid_3

0.949

0.840

n.a.

0.829

0.927

Corona_pk3

Pk

0.579

0.646

0.674

0.678

0.705

CPEB3_ribozyme

Pk

0.756

0.756

0.663

0.756

0.612

Gammaretro_CES

0.983

0.948

0.983

0.935

0.983

Hammerhead_1

1.000

0.474

0.621

0.831

0.614

Hammerhead_3

1.000

0.960

1.000

1.000

1.000

HDV_ribozyme

Pk

0.709

-0.018

0.784

0.388

0.396

IRES_c-myc

-0.004

0.079

0.286

-0.002

0.350

R2_retro_el

1.000

0.842

0.946

0.987

0.890

RNAIII

0.467

0.595

n.a.

0.479

0.830

RNase_MRP

Pk

0.626

0.423

0.457

0.271

0.575

rne5

0.994

0.969

0.975

0.762

0.923

RydC

Pk

0.466

0.562

0.608

0.466

-0.020

s2m

0.739

1.000

0.774

0.652

0.861

Telomerase-cil

1.000

0.937

0.921

1.000

0.953

Telomerase-vert

pk

0.918

0.751

n.a.

n.a.

0.820

Vimentin3

0.741

-0.016

0.184

0.771

0.629

Y

1.000

1.000

0.925

1.000

1.000


mean

0.759

0.651

0.703

mean

knetfold

0.750

0.645

0.680

0.696

mean

pfold

0.756

0.635

0.693

0.682

0.673


Performance comparisons on the RNA STRAND-Rfam dataset. We list the MCC for different alignments. Best performance indicated in bold, n.a. means that data is not available due to length restrictions on the respective server, pk denotes structures that contain a pseudo-knot. As there are many pseudo-knotted structures in this dataset, KNetFold was used in the "Check pseudoknot" mode. The MCCs take into account the pseudo-knots.

Bernhart et al. BMC Bioinformatics 2008 9:474   doi:10.1186/1471-2105-9-474

Open Data