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Examples

Distance Table

The computation of a distance table can be used to build a phylogenetic or a clustering tree. The following two examples present the trees resulting from the computation of two distance tables, the first one on microRNA and the second on snoRNA of the HACA-box subfamily. The two trees show that with some exceptions, the RNA are being grouped in subtrees of same subfamilies.

For each tree, the 100 structures were randomly selected in the data base by a script. The distance table was then computed using the algorithm of RNAStrAP1. Then, this table was given to BioNJ2 to compute a tree. Finaly, the tree was rendered and annotated using TreeDyn3.

miRNA
Figure 1: clustering tree infered by RNAStrAP+BioNJ for the microRNA selection
Legend: each color correspond to one miRNA family (warning: some colors are similar but different!). Black is used when only 1 member of a family is present. Redish taxa with black background are not correctly clustered.


HACA-box
Figure 2: clustering tree infered by RNAStrAP+BioNJ for the snoRNA (HACA-box subfamily) selection.
Legend: each color correspond to one snoRNA family (warning: some colors are similar but different!). Black is used when only 1 member of a family is present.


Source data:
  1. V.Guignon, C.Chauve and S.Hamel, An edit distance between RNA stem-loops, Lecture Notes in Computer Science 3772 (String Processing and Information REtrival), pp. 335-347, 2005. (PDF)
  2. Gascuel O. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol. Evol. 1997, Jul;14(7):685-95. (PubMed)
  3. Chevenet F., Brun C., Banuls AL., Jacq B., Chisten R. TreeDyn: towards dynamic graphics and annotations for analyses of trees. BMC Bioinformatics. 2006, Oct 10;7:439. (PubMed)