Table 5

SPS scores for BRAliBASE version 2.1

SPS

Method

Time

N = 2

N = 3

N = 5

N = 7

N = 10

N = 15

ClustalW (iterative)

52 minutes

0.796

0.810

0.828

0.837

0.850

0.853

ProbConsRNA

33 minutes

0.836

0.855

0.879

0.890

0.899

0.907

G-INS-i

8.8 minutes

0.837

0.851

0.874

0.890

0.901

0.913

LaRA 1.31

5.5 days

0.798

0.830

0.864

0.883

0.898

0.913

Murlet

2.5 weeks

0.843

0.863

0.886

0.897

0.906

0.915

MXSCARNA 2

4.2 hours

0.850

0.866

0.884

0.894

0.907

0.914

RNA Sampler (fast)

8.2 days

0.787

0.801

0.824

0.828

0.841

0.855

RNAsampler

2.9 weeks

0.785

0.812

0.839

0.850

0.858

0.869

X-INS-i-larapair

5.4 days

0.837

0.869

0.896

0.909

0.919

0.930

X-INS-i-scarnapair

18 hours

0.856

0.876

0.902

0.913

0.922

0.931

# of alignments

8,976

4,835

2,405

1,426

845

503

(used for Wilcoxon test)

(8,976)

(4,832)

(2,399)

(1,420)

(836)

(491)

The highest scores within each group (N = 2, 3, 5, 7, 10, 15) are underlined. The scores close to the highest (p > 0.01 in the Wilcoxon test) are shown in bold. As Murlet and RNA Sampler aborted for a small number of datasets, the Wilcoxon test was carried out using a limited set (the numbers of alignments are in parentheses), for which every method returned an alignment.

Katoh and Toh BMC Bioinformatics 2008 9:212   doi:10.1186/1471-2105-9-212