Table 3

Results using alternative MCC and alignment

Program or variant

MCC

Other MCC

Clustal MCC


RNAalifold 2002

0.831

0.814

0.708

RNAalifold new

0.845

0.819

0.711

RNAalifold RIBOSUM

0.937

0.871

0.788

RNAalifold 2002 centroid

0.828

0.815

0.693

RNAalifold new centroid

0.848

0.834

0.712

RNAalifold RIBOSUM centroid

0.934

0.896

0.780

Pfold

0.765

0.739

0.601

KNetFold

0.866

0.808

0.761

McC_mea

0.837

0.816

0.716


Performance comparisons on the CMfinder-SARSE dataset. We list the mean MCC for different programs. Best performance indicated in bold. Other MCC is the variant counting every wrongly predicted pair as false positive, Clustal MCC is the MCC as introduced by Gardner et al. [39] applied to alignments realigned using Clustal [40].

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

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