Computational protocol: Telomere length kinetics assay (TELKA) sorts the telomere length maintenance (tlm) mutants into functional groups

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Protocol publication

[…] All the data measured by TelQuant analysis was analysed using Excel. Clusters were made using CLUSTER3 () (http://bonsai.hgc.jp/∼mdehoon/software/cluster/) and viewed by the JAVA TREEVIEW program (http://jtreeview.sourceforge.net/) (). Preliminary analysis of mutants affecting known protein complexes showed that this method gave the best results. The 30 mutants analysed here were chosen based on the following criteria: (i) short mutants were analysed; (ii) one representative of each known complexes was chosen (with the exception of the mutants used for calibrating TELKA, which belonged to known complexes); (iii) their final telomere length was at least 10% shorter than the wt length. Comparing the intra-cluster Euclidian distances in the clusters obtained to a set of a million random permutations of the dataset resulted in an empirical P-value <10−6. […]

Pipeline specifications

Software tools Cluster, TreeView, JTreeView
Application Phylogenetics
Organisms Saccharomyces cerevisiae