Automatic generation of pseudoknotted RNAs taxonomy

BMC Bioinformatics

Table 2 Results of the evaluation framework applied to the 16S rRNA benchmark in which molecules are divided into Archaea, Bacteria and Eukaryota. Single linkage was used in clustering

	Genus	PSMAlign	ASPRAlign	PskOrder	RAG-2D
Archaea
Rand index	0.514	0.594	0.920	0.601	0.547
Homogeneity	0.037	0.288	0.833	0.118	0.127
Completeness	0.073	0.427	0.778	0.230	0.099
Bacteria
Rand index	0.407	0.495	0.461	0.302	0.696
Homogeneity	0.100	0.357	0.276	0.074	0.240
Completeness	0.206	0.843	0.564	0.279	0.215
Eukaryota
Rand index	0.410	0.450	0.457	0.237	0.611
Homogeneity	0.110	0.234	0.231	0.065	0.218
Completeness	0.296	0.591	0.560	0.406	0.311

The highest score for each row is written in bold
The scores of the three metrics rand index, homogeneity and completeness are shown where the taxa were constructed basing on dissimilarity matrices taken from genus topological invariant (Genus), PSM (PSMAlign tool) ASPRA distance (ASPRAlign tool), Pseudoknot Order (PSkOrder) and RNA as Graph Fiedler Vector approach (RAG-2D)

ISSN: 1471-2105