UC Santa Cruz UC Santa Cruz Electronic Theses and Dissertations Title Bioinformatic Investigations in Marine Microbial Ecology Permalink https://escholarship.org/uc/item/61q69869 Author Heller, Philip Publication Date 2014 License https://creativecommons.org/licenses/by-nc-nd/4.0/ 4.0 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA SANTA CRUZ BIOINFORMATIC INVESTIGATIONS IN MARINE MICROBIAL ECOLOGY A dissertation submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in BIOINFORMATICS by Philip Heller December 2014 The Dissertation of Philip Heller is approved: ____________________________________________________ Professor Jonathan Zehr, chair ____________________________________________________ Professor Josh Stuart ____________________________________________________ Rex Malmstrom, Ph.D. ________________________________________________ Tyrus Miller Vice Provost and Dean of Graduate Studies Copyright © by Philip Heller 2014 Table of Contents Table of Contents ............................................................................................................. iii List of Tables and Figures ............................................................................................... v Abstract ............................................................................................................................. vii Introduction ........................................................................................................................ 1 Background ................................................................................................................................. 1 nifH sequence retrieval and curation ................................................................................. 4 Metagenomics of UCYN-A2 ..................................................................................................... 6 Transcriptomics and diel expression of cyanobacteria ............................................... 7 Chapter 1: ARBitrator: A software pipeline for on-demand retrieval of auto-curated nifH sequences from GenBank1 ....................................................... 15 Abstract ....................................................................................................................................... 16 Introduction .............................................................................................................................. 17 System and Methods ............................................................................................................... 21 Design Criteria .......................................................................................................................... 21 Algorithm ................................................................................................................................................. 23 Implementation .................................................................................................................................... 23 Tuning ....................................................................................................................................................... 26 Error rates ............................................................................................................................................... 27 Extension beyond nifH ....................................................................................................................... 28 Results ......................................................................................................................................... 29 Sequences Retrieved on Nov 20, 2012 ....................................................................................... 29 Error Rates .............................................................................................................................................. 30 Comparison to other nifH databases ........................................................................................... 31 nifD results .............................................................................................................................................. 32 Discussion .................................................................................................................................. 32 Necessity for Both Quality and Superiority Criteria ............................................................. 33 Error Rates .............................................................................................................................................. 34 Comparison to other nifH databases ........................................................................................... 35 Acknowledgements ................................................................................................................. 37 References .................................................................................................................................. 38 Supplementary Appendix A: Procedure for updating an existing ARB database with ARBitrator output .......................................................................................................... 42 Figures ......................................................................................................................................... 45 Chapter 2: Metagenomics of Uncultivated UCYN-A Cyanobacteria1 .............. 50 Preface ......................................................................................................................................... 51 Comparative genomics reveals surprising divergence of two closely related strains of uncultivated UCYN-A cyanobacteria .............................................................. 53 ABSTRACT ............................................................................................................................................... 53 Introduction ............................................................................................................................................ 54 iii Materials and Methods ...................................................................................................................... 57 Results ....................................................................................................................................................... 61 Discussion ................................................................................................................................................ 66 Conclusions ............................................................................................................................................. 72 Conflict of Interest ............................................................................................................................... 73 Acknowledgements ............................................................................................................................. 74 References ............................................................................................................................................... 74 Supplemental Methods ...................................................................................................................... 80 Supplemental References ................................................................................................................. 85 Figures and Tables ............................................................................................................................... 87 Addendum to Chapter 2: 16S Ribosomal RNA Assembly ........................................... 99 Addendum Introduction ................................................................................................................... 99 Addendum Methods .......................................................................................................................... 100 Addendum Results ............................................................................................................................. 102 Addendum Discussion ...................................................................................................................... 103 Addendum References ..................................................................................................................... 107 Addendum Figures ............................................................................................................................ 109 Chapter 3 – Dexter: A tool for exploring diel expression data sets ............. 112 Abstract .................................................................................................................................... 112 Background ............................................................................................................................ 113 System and Methods ............................................................................................................ 120 Requirements ........................................................................................................................ 120 Workflow ............................................................................................................................................... 121 Application to Operon Prediction 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