tensor decomposition reveals concurrent evolutionary convergences and divergences and correlations with structural motifs in ribosomal rna张量分解显示并行进化和相关性的共同点和不同点在核糖体rna结构图案.pdfVIP

Tensor Decomposition Reveals Concurrent Evolutionary Convergences and Divergences and Correlations with Structural Motifs in Ribosomal RNA 1 2 1,3 4 Chaitanya Muralidhara , Andrew M. Gross , Robin R. Gutell , Orly Alter * 1 Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America, 2 Bioinformatics and Systems Biology Program, University of California at San Diego, San Diego, California, United States of America, 3 Section of Integrative Biology and Center for Computational Biology and Bioinformatics, University of Texas at Austin, Austin, Texas, United States of America, 4 Scientific Computing and Imaging (SCI) Institute and Departments of Bioengineering and Human Genetics, University of Utah, Salt Lake City, Utah, United States of America Abstract Evolutionary relationships among organisms are commonly described by using a hierarchy derived from comparisons of ribosomal RNA (rRNA) sequences. We propose that even on the level of a single rRNA molecule, an organism’s evolution is composed of multiple pathways due to concurrent forces that act independently upon different rRNA degrees of freedom. Relationships among organisms are then compositions of coexisting pathway-dependent similarities and dissimilarities, which cannot be described by a single hierarchy. We computationally test this hypothesis in comparative analyses of 16S and 23S rRNA sequence alignments by using a tensor decomposition, i.e., a framework for modeling composite data. Each alignment is encoded in a cuboid, i.e., a third-order tensor, where nucleotides, positions and organisms, each represent a