The process stops either when all herds are clustered, or when the CD of comparison between the clustered herds and each of the remaining herds are all below the fixed a priori threshold χ.
Third, a standard set of Representative Proteomes (RPs) would enable the scientific community to make direct comparison between clusters and annotations produced by various methods.
For example, every pairwise comparison between clusters should be informative as well as their holistic interpretation, foreshadowing the utility of this methodology for exploratory data analysis.
The annotation of genes was performed using the program Blast2GO (http://www.blast2go.org/), which provides a comparison between clusters of sequences obtained from public databases.
Even if the comparison between clustering algorithms is a complex task, we observed that k-means approach is more efficient to conserve gene associations.
Comparison between clustering analysis (UPGMA) and PCoA (Additional file 2) showed that the pattern of clustering the taxa was similar with both analyses: The individuals collected in the Gulf of Thailand clustered as single clade, whereas individuals collected in the Andaman Sea grouped together.
Clusters 2 and 3 were significantly different from one another (paired t test, t6 = 2.476, p = 0.048), but no other pairwise comparison between clusters was statistically different (paired t tests, 1 vs. 2: t6 = -1.138, p = 0.299; 1 vs 3: t6 = 1.341, p = 0.228).
Through cross-species comparison between two clustered groups, retrieving conserved or exclusive SSR motifs could help biologists in choosing significant biomarkers from a previously defined gene set before performing biological experiments.
