an automated phylogenetic tree-based small subunit rrna taxonomy and alignment pipeline (stap)一个自动化的系统发育树小亚基rrna分类法和对齐管道(堵塞).pdfVIP

An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP) 1 1,6 4,5 1,2,3 Dongying Wu *, Amber Hartman , Naomi Ward , Jonathan A. Eisen 1 UC Davis Genome Center, University of California Davis, Davis, California, United States of America, 2 Section of Evolution and Ecology, College of Biological Sciences, University of California Davis, Davis, California, United States of America, 3 Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, California, United States of America, 4 Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, United States of America, 5 Center of Marine Biotechnology, Baltimore, Maryland, United States of America, 6 The Johns Hopkins University, Department of Biology, Baltimore, Maryland, United States of America Abstract Comparative analysis of small-subunit ribosomal RNA (ss-rRNA) gene sequences forms the basis for much of what we know about the phylogenetic diversity of both cultured and uncultured microorganisms. As sequencing costs continue to decline and throughput increases, sequences of ss-rRNA genes are being obtained at an ever-increasing rate. This increasing flow of data has opened many new windows into microbial diversity and evolution, and at the same time has created significant methodological challenges. Those processes which commonly require time-consuming human intervention, such as the preparation of multiple sequence alignments, simply cannot keep up with the flood of incoming data. Fully automated methods of analysis are needed. Notably, existing automated methods avoid one or more steps that, though computationally costly