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DACIDR for Gene Analysis

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.

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DACIDR for Gene Analysis

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  1. 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 Visualization Streaming Multidimensional Scaling Simplified Flow Chart of DACIDR

  2. 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

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

  4. 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

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