DACIDR for Gene Analysis

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Presentation transcript:

DACIDR for Gene Analysis Deterministic Annealing Clustering and Interpolative Dimension Reduction Method (DACIDR) Use Hadoop for pleasingly parallel applications, and Twister (replacing by Yarn) for iterative MapReduce applications Pairwise Clustering All-Pair Sequence Alignment Streaming Visualization Multidimensional Scaling Simplified Flow Chart of DACIDR

PWA vs MSA Pairwise sequence alignment (PWA) is much faster and has very high correlation with multiple sequence alignment (MSA). The comparison using Mantel between distances generated by three sequence alignment methods and RAxML

Summarize a million Fungi Sequences Spherical Phylogram Visualization RAxML result visualized in FigTree. Spherical Phylogram visualized in PlotViz

MDS methods Sum of branch lengths will be lower if a better dimension reduction method is used. WDA-SMACOF finds global optima Sum of branch lengths of the SP generated in 3D space on 599nts dataset optimized with 454 sequences and 999nts dataset