SSPcompare is a modest tool that takes a library of known sequence-structure pairs, e.g. in RNAstrand (Andronescu et al. 2008) or FR3D (Sarver et al. 2008) format as well as in the formats produced by different RNA secondary structure prediction tools. In this iteration, an additional option is to read TrainingData created by Höner zu Siederdissen et al. (2011) .

Parts of this tool (mostly, the different accuracy measures) will be merged with a biostatistics library.

The tool is used as part of the training process to provide information on how far the prediction has progressed.


Andronescu, Mirela, Vera Bereg, Holger Hoos, and Anne Condon. 2008. RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database. BMC Bioinformatics 9: 340. doi:10.1186/1471-2105-9-340.

Höner zu Siederdissen, Christian, Stephan H. Bernhart, Peter F. Stadler, and Ivo L. Hofacker. 2011. A Folding Algorithm for Extended RNA Secondary Structures. Bioinformatics 27: 129–36. doi:10.1093/bioinformatics/btr220.

Sarver, Michael, Craig L. Zirbel, Jesse Stombaugh, Ali Mokdad, and Neocles B. Leontis. 2008. FR3D: Finding Local and Composite Recurrent Structural Motifs in RNA 3D Structures. Journal of Mathematical Biology: 215–52.