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Web-Based Genome Portal for Haptophytes

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Web-Based Genome Portal for Haptophytes CALIFORNIA STATE UNIVERSITY SAN MARCOS PROJECT SIGNATURE PAGE PROJECT SUBMJTTED IN PARTIAL FULFILLMENT OF THE REQUJREMENTS FOR THE DEGREE MASTER OF SCIENCE IN COMPUTER SCIENCE PROJECT TITLE: Web-Based Gnome Portal for Haptophytcs AUTHOR: Taniya Rohrnetra DATE OF SUCCESSFUL DEFENSE: August 3, 2017 THE PROJECT HAS BEEN ACCEPTED BY THE PROJECT COMMITTEE IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE IN COMPUTER SCIENCE. ~A/1/,~~,-----o· 5;,f- Dr. Xiaoyu Zhang ï PROJECT COMMITTEE CHAIR SIGNATURE DATE Dr. Betsy Read gf-&17 PROJECT COMMITIEE MEMBER DATE Dr. Ahmad Hadaegh ~,9 3 :> .QD, -:J PROJECT COMMITTEE MEMBER DATE Web-based Genome Portal for Haptophytes Taniya Rohmetra In Fulfillment of the Master of Computer Science California State University San Marcos June, 2017 I Abstract This project is a web portal for the Genome Portal for Haptophytes. The web portal has been created keeping in mind the requirements of the researchers in their study of Genomes. This portal focuses mainly on Haptophytes, three of them to be precise; Emiliania huxleyi, Gephyrocapsa oceanica and Isochrysis galbana. A few tools have been embedded into the web portal to help study the genomes. These tools include JBrowse, BLAST and Synteny. The JBrowse that is embedded is a genome browser that helps to explore the genome and gives specific information about each gene. The Basic Local Alignment Search Tool (BLAST) is used for the sequencing search of the bioinformatics programs. The FASTA file i.e., a text format that represents the nucleotides or peptide sequences for each of the three genomes has also been made available for download via the web portal. II Acknowledgements It is my pleasure to extend my deepest gratitude to my committee members, Dr. XiaoyuZhang, Dr. BetsyRead and Dr. AhmadHadaegh for sharing their wisdom during this study. I am extremely thankful to them for their time and valuable suggestions to better this study. I am forever thankful to my parents and my sister for being my greatest support and want to acknowledge them for having encouraged me to look forward and grab good opportunities that come my way. III Table of Contents 1. INTRODUCTION ............................................................................................................. - 5 - 2. BACKGROUND ................................................................................................................ - 5 - 2.1 PLATFORMS FOR COMPARATIVE GENOMICS ............................................................................................. - 5 - THIS PROJECT WAS BUILT USING THE SERVICES PROVIDED BY ................................................................................ - 5 - 2.2 TOOLS FOR COMPARATIVE GENOMICS ...................................................................................................... - 6 - 3. DESIGN AND USER INTERFACE ................................................................................ - 7 - 3.1 SITE MAP .................................................................................................................................................. - 7 - 3.2 WEB INTERFACE ....................................................................................................................................... - 7 - 3.3 TOOL PAGES ........................................................................................................................................... - 11 - 3.3.1JBrowse .................................................................................................................................................. - 11 - 3.3.2 BLAST .................................................................................................................................................. - 12 - 3.3.3 Synteny ................................................................................................................................................. - 13 - 4. USER GUIDE .................................................................................................................. - 15 - 4.1 USER LOGIN ............................................................................................................................................ - 15 - 4.2 JBROWSE ................................................................................................................................................ - 18 - 4.3 BLAST ................................................................................................................................................... - 19 - 4.4 DOWNLOAD DATA .................................................................................................................................. - 21 - 4.5 SYNTENY ................................................................................................................................................ - 23 - 5. IMPLEMENTATION AND ANALYSIS ...................................................................... - 25 - 5.1 MODEL-VIEW-CONTROLLER STRUCTURE ............................................................................................... - 25 - 5.2 EMBEDDING OF COGE TOOLS ................................................................................................................. - 29 - 5.3 OTHER IMPLEMENTATION ISSUES ........................................................................................................... - 30 - 6. CONCLUSION ................................................................................................................ - 32 - 7. REFERENCES ................................................................................................................ - 33 - 7.1 APPENDIX ....................................................................................................................................................... - 35 - IV List of Figures Figure 1 Site Map for the web site .............................................................................................. - 7 - Figure 2 Homepage of web site .................................................................................................. - 8 - Figure 3. CoGe authentication using Cyverse services .............................................................. - 9 - Figure 4 Genome page (Emiliania Huxleyi) ............................................................................. - 10 - Figure 5 JBrowse (Emiliania Huxleyi) .................................................................................... - 11 - Figure 7 BLAST (Eniliania Huxleyi) ....................................................................................... - 12 - Figure 8 Download page for FASTA file (Emiliania Huxleyi) ................................................ - 13 - Figure 9 Synteny page (Emiliania Huxleyi with Gephyrocapsa Oceanica) ............................. - 14 - Figure 10 Example of MVC (Web Portal) ................................................................................ - 26 - Figure 11 file directory (Web Portal) ........................................................................................ - 27 - V 1. Introduction The goal of this project is to build a Genome portal for Haptophytes to support the comparative genomic research of the biotechnology faculty at CSUSM and general community. The developed portal would make the data readily available to the people and using that data, they can run the BLAST search, JBrowse and Synteny tool easily. The website concentrates on three sister species; Emiliania huxleyi, Gephyrocapsa oceanica and Isochrysis galbana. Emiliania huxleyi also known as “Ehux” [2] is one of the most populous coccolithophore, meaning they can produce a shell alike exoskeleton which has plates called coccoliths. Moreover, it is considered as a ubiquitous species and has one of the largest temperature ranges of all the coccolithophores. They are found in the contemporary oceans and contribute heavily to the global biogenic calcite production. Despite several existent coccolithophore species available, because of the global significance and its versatility to fit in wide range of environmental condition, E. huxleyi is used as a model species in many physiological, ecological, oceanographic, palaeoceanographic, and modelling studies. One of the productions of Emiliania huxleyi is due to photosynthesis, that is, it is one of the sinks for carbon dioxide. It is considered one of the important sources of carbon dioxide outside of the ocean. - 1 - Gephyrocapsa oceanica is a cosmopolitan bloom-forming coccolithophore species belonging to the haptophyte order Isochrysidales and family Noëlaerhabdaceae. Exclusively pelagic, G. oceanica is commonly found in modern oceans and in fossil [17] assemblages. G. oceanica evolve generally in response to elevated CO2 where it show a direct response to selection, but show little specific adaptation in terms of differences in phenotype.[18] Emiliania huxleyi and Gephyrocapsa oceanica are abundant coccolithophore morpho- species that play key roles in ocean carbon cycling due to their importance as both primary producers and cal-cifiers.[19] Gephyrocapsa oceanica and its sister species Emiliania huxleyi, both shows no significant ultrastructural differences in the calcifying diploid stage or the haploid phase. Isochrysis galbana is free living marine unicellular phytoflagellate of the order Chrysomonadales. They are small and are motile with flagella; they are also digestible by the small invertebrates as their cell wall is
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