Because the software Cytoscape [ 28] offers highly flexible network visualization, we provide all of our results in a Cytoscape compatible format as supplementary data.
Complex dendrograms were built using the iTOL service (60, 62) on distance matrices exported online in the Nexus format and other supplementary data generated online.
The protein information retrieved for DMS3 (defective in meristem silencing 3), KTF1, DCL, and RDM1 (RNA-directed DNA methylation 1) is given in supplementary tables S2 S5, Supplementary Material online, respectively, and all protein sequences from each group are given in FASTA format in the Supplementary data file S1, Supplementary Material online.
The complete alignment in clustalw format is shown in Supplementary Data S1.
The complete definition of the proposed DASINT XML format can be found in Supplementary Data File 2. A DASMI server responds to an interaction request by providing interaction data in the DASINT XML format defined above.
A more detailed differentiation of DASINT from alternative data exchange formats can be found in Supplementary Data File 1. Figure 3c shows an illustration of the DASINT XML Schema Definition.
SNP variants detected among our genomes and used for downstream analysis are reported in supplementary data, Supplementary Material online, in a tab-delimited format.
Supplementary Text S1 S5 in ' Supplementary Data' provides reference gene trees in extended Newick format (NHX) with annotated gene duplications, lists of gene pairs with annotated gene relationships and a list of genes that were excluded from the analysis, e.g. fragments.
The majority of the published data is in unstructured formats such as images, abbreviations and supplementary data; therefore, the data is not searchable.
All of the supplementary data, wherever applicable, are available to download as GFF format files from Spud DB site " http://potato.plantbiology.msu.edu/".msu.edu/
Fig. 1 Supplementary data of a journal article (case study I) depicting the computed molecular data format, the contents in the highlighted text are required for the re-computation of data.
