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Four of the eight expanded clusters contained genes with no blast hits (e value ≤ 1e 20).
To remedy over-splitting, the expanded clusters were merged using a modification of the procedure described previously [ 48].
The expanded clusters in Figure 1 are highly enriched in trypomastigote-upregulated trans-sialidases (TS) and mucins.
The PSSMs for the expanded clusters were generated by aligning the member sequences using MUSCLE followed by using the PSSMs as queries for PSI-BLAST searches against the database of all mitochondrial sequences in the expanded clusters with an e-value threshold of 0.01.
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Output: expanded cluster.
Therefore, taking the aforementioned factors into consideration, the size of the expanded cluster,, should satisfy (7).
Additionally, the radius of the expanded cluster should also be smaller than the Euclidian distance threshold (6).
In Step 3, each cluster is expanded by adding a number of virtual colours, which are not present in the original image and near the centroid of the cluster, in order to form an expanded cluster with colour.
We also require that the size of the expanded cluster still equals a power of 2, in order to avoid redundancy.
Six (11%) were identified as cluster-associated patients on the basis of the expanded cluster case definition.
This final set of mutants is a putative motif and the expanded cluster is its target gene cluster.
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