clusterId is the unique ID for the orthologous clusters detailed in the method section.
In term of methods, as done by the Thomas'group, our prediction of the presence of zinc finger genes was based on TBLASTN searches of the chimpanzee regions which are syntenic to the human clusters (detailed in Tadepally et al[ 2]).
Figure 3B shows the 20 clusters identified using our correlation-based clustering approach to measure the similarity of VRVs, at a minimum correlation coefficient threshold of 0.75 (see Figure S2 and Table S1 for additional cluster details).
A network, such as PHPN, can take an extraordinarily complex system and reduce it to a relatively simple form, revealing underlying connections and important clustering details that would not be evident from studying individual or non-complex relationships among traits [ 8].
By descending the hierarchy and showing the actual members of each cluster, detailed information can still be intuitively shown at a particular scale (e.g. the dotted arrows and regions in Supplementary Figure S1).
The strategy about reads clustering detailed in Algorithm 2 is as follows: take a sequence from reads randomly as a cluster center; find all sequences sharing a k-mer with the center; and validate each sequence by extend k-mer to seeds.
Spark streaming measurements were conducted with the Test client, and Spark algorithms (Fig. 1), which were submitted to Spark's standalone cluster manager (in cluster mode) (details in Figs. 16, 17).
The discretization criterion and stopping criterion of these algorithms are based on the NAsso criterion (see "Measures with clusters" for details).
Because the minimum normalized cut criterion is equivalent to the maximum normalized association criterion (see "Measures with clusters" for details), to design the stopping criterion, this normalize association criterion is chosen in this study.
We repeated the entire modeling process with different settings for the discrimination distance that defines clonal clusters (see details in Materials and methods) confirming the robustness of the estimated clonality rate.
