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.
Dr. Xiaoyu Zhang ~A/1/,~~,-----o· ï 5;,f- 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 deprived of calcium carbonated cell covering.
It is an outstanding food for various bivalve larvae and is now widely cultured for use in the bivalve aquaculture industry. Isochrysis has been widely used as a mariculture feed due
to its high content of long chain polyunsaturated fatty acids (PUFAs) (Jeffrey et al., 1994).
They have ability to produce the polyunsaturated fatty acid docosahexaenoic acid (DHA),
one of the n-3 fatty acids believed to provide health benefits associated with the
consumption of certain marine fish and their oils. DHA, a C22-polyunsaturated fatty acid,
and its derivatives help prevent and treat pathologies.[21]
- 2 -
Emiliania huxleyi and Isochrysis galbana are the living Isochrysidales and both Emiliania huxleyi and Isochrysis galbana produce a set of polyunsaturated long-chain (C37–39) alkenones, alkenoates, and alkenes (PULCA). These biomarkers are widely used for palaeothermometry, but the biosynthesis and cellular location of these unique lipids remain largely unknown.[22]
This project focuses on providing a single portal for various tools that are required for the
research purpose of these genomes. These tools include JBrowse, BLAST, Synteny. A
FASTA file is available for download for each of these genomes [6]. Emiliania huxleyi,
Gephyrocapsa oceanica and Isochrysis galbana are all Haptophytes. Among these
isochrysisgalbana is widely used in the aquaculture industry.
The website has been developed entirely using PHP, HTML5, CSS and Javascript.
Embedding of the different tools into the website is done using iframes. The access is
granted for using the tools once the user has logged into the CoGe site as the data being
used is secured on the CoGe database and will be so till it is published, once published the
user will no longer have to login to access any of the data as it will then be publicly
available. Moreover, detailed information of the three genomes can be fetched, and
weighted against each other by leveraging Synteny. The comparison of the genomes can
be viewed graphically as well. The tools deployed/incorporated on the website are easy to
use for a novice user.
The rest of this paper is organized as follows, Section 2 provides the related work and
explains the background, Section 3 illustrates the user interface and the user guide which
- 3 - would help the readers in better understanding of the website. Next, we detail the implementation of the functions and finally we conclude the work and outline the future scope of this project and how it can be improved.
- 4 -
2.Background
2.1 Platforms for Comparative Genomics
This project was built using the services provided by
CoGe: COMPARATIVE GENOMICS (htpps://genomevolution.org/coge/). CoGe[3] is a well-known online existing platform widely used for making retrieval and comparisons of genomic information and sequence data. The main design principle of CoGe is to maintain a simple and straight forward approach, starting from the infrastructure to the web-based tools rendering it user-friendly.
CoGe has been chosen for this project because it is easy and quick to use even though it stores multiple version of multiple genomes from multiple organisms in a single platform.
The comparison of genomes is done using any algorithm and the result is usually a visual representation to make the identification quick and easy. The analysis is done through the web-based tools and large-scale comparisons are usually done using programming. The different parts of CoGe used different languages per what suits them aptly.
There are various other sites like CoGe, like VISAT[14] or OMIC tools etc. VISTA is a platform where comprehensive programs and databases are used for the analysis of genomic sequences. There are couple of ways in which VISTA can be used. The first way is where you can submit your own alignments and sequences for analysis. Another way to use it is where you can examine pre-computed genome alignments of various species.
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OMIC[15]tools are an interactive worldwide user community like CoGe. It links curators who submit, categorize and review tools to users. Using the review tools, the users can give their feedback and reviews.
2.2 Tools for Comparative Genomics
Several tools were made available in this web portal for Haptophytes.
JBrowse is a browser for the genomes that has a completely dynamic AJAX interface. It is a successor to GBrowse. JBrowse is known for efficiently handling large datasets, is very fast and performs most of its work in the user’s web browser directly with little or no requirements from the server.
BLAST stands for Basic Local Alignment Search Tool [4]. It is an algorithm that is primarily used to compare the information of the biological sequences, like the nucleotides of the DNA sequences or the amino acid sequences of the proteins.
Synteny[5] is another tool that has been added to the website. It is a deduction that two or more genomic regions have been derived from an ancestral genomic region. This is used by the biologist to compare two sets of chromosomes. In our website, the comparison of the three genomes with each other has been incorporated, hence forming a total of three
pairs of comparison. When one selects either of the three comparisons, a graph is shown
that shows the similarity of the genomes. This graph is used to study the comparison of the
two genomes.
- 6 -
3.Design and User Interface 3.1 Site Map
The URL to the web portal is: bioinfo.csusm.edu.
It is imperative to understand the nuances of site map as it gives a clear picture of the
website designing aspect before going further. Primarily, after logging into CoGe, the access to the data of the three genomes i.e.,Emiliania huxleyi, Gephyrocapsa oceanica and isochrysis galbanaisavailable.The data of each of these genomes can then be used in any of the available tools on the website. i.e., JBrowse, BLAST and Synteny. The FASTA file of each of the genomes can also be downloaded from the website. The sitemap for the website is as seen in fig.,1.
Figure 1 Site Map for the web site 3.2 Web Interface
The home page of the website is displayed in fig.,2. It shows the images of three genomes
i.e., Emiliania huxleyi, Gephyrocapsa oceanica and isochrysis galbana. There is a google
- 7 - search bar on the page, to look for any additional information. It is important that one must first login into CoGe before accessing any of the genome files, as the files and data being used are secured and not accessible by public till the research is published, once the research is published there will not be any need to login into the CoGe server as the data will be made public. The Login option is on the top left corner of the home page. It redirects to the CoGe Login page, where one can enter the credentials and login, as shown in fig.,3.
Figure 2 Homepage of web site
- 8 -
Figure 3. CoGe authentication using Cyverse services
After gaining the access to CoGe, one can return to the home page and can then select
one of the three genomes. When one clicks on our choice of the genome, it opens a new
page with information on that genome and tools that will help in the better understanding
of it. There are various tools like JBrowse, BLAST and Synteny. There is also a FASTA
file available for download. The layout of the page is shown in fig.,4. The menu bar on
top shows the different tools available and the option to go back to the home page. There
is an image of the Emiliania Huxleyigenome and some information as to what it is. There
is also a Google search bar available on this page. The “Home” option in the menu bar on
top of the page can be used to go back to the home page. The menu bar stays consistent
on every page, to allow the user to access any other tool or go back to the home page
from the current page.
- 9 -
Figure 4 Genome page (Emiliania Huxleyi)
- 10 -
3.3 Tool Pages
3.3.1JBrowse
Figure 5 JBrowse (Emiliania Huxleyi) JBrowser is a genome browser that has been embedded in our website, this tool is built using HTML 5 and JavaScript. JBrowse is used to explore the genomes[7]. This tool allows
us to zoom in and out of each gene and when one clicks on any gene, it gives us a pop-up
message with all the information about that gene. fig 4, shows the JBrowse tool. The
“Home” option in the menu bar on top of the page can be used to go back to the home page.
The menu bar stays consistent on every page, to allow the user to access any other tool or
go back to the home page from the current page.
- 11 -
3.3.2 BLAST
BLAST is another tool that has been embedded into our website for comparing the primary information on the biological sequence. fig, 6 shows the BLAST tool on the website.
Figure 6 BLAST (Eniliania Huxleyi) The BLAST tool requires the user to input a FASTA file, for it to give the desired information[4]. When a user goes to the Blast tool of either of the three genomes, then the user can enter the FASTA sequence in the Query sequence text box. Once the FASTA file has been entered, then the user can proceed further and click the CoGe blast. Once the
BLAST is complete, the HSP (High Scoring Pair) count is seen and the HSP genomic visualization graph is generated along with the HSP table. When the user clicks on the download option from the menu bar on top of the page, the user gets directed to a page where the FASTA file of the genome is available for download. Fig, 7 shows the Download
- 12 - page view. When the user clicks on the blue link of the FASTA file, the FASTA file starts to download.
Figure 7 Download page for FASTA file (Emiliania Huxleyi) 3.3.3 Synteny
This website has also been embedded with the Synteny tool. Synteny compares each genome individually with the other genomes. The user can select the two genomes that should be compared with. A graph is generated to illustrate the similarity between the two
genomes being compared. The use of Synteny is necessary as it is useful in defining
functional relationship between genes[5].
Fig, 8 shows the Synteny tool that is being used to compare Emiliania Huxleyi with
Gephyrocapsa Oceanica.
- 13 -
Figure 8 Synteny page (Emiliania Huxleyi with Gephyrocapsa Oceanica)
- 14 -
4. User Guide Users may perform several analyses of available Haptophyte genomes, while new tools
may be added in the future. This chapter provides a user guide to give a stepwise overall
view of the website.
4.1 User Login
Currently a user must login first to access data on the portal. Step wise implementation is
shown below
Steps1 to 3 show procedures for user login and selecting a species to access.
STEP 1: Click on Login and a CoGe login page will open.
STEP 2: Login into the CoGe site.
- 15 -
STEP 3: Select a Genome from the three options.
STEP 4: If Emiliania Huxleyi is selected, its information will be displayed as shown.
- 16 -
STEP 5: Click on JBrowse.
- 17 -
4.2 JBrowse
The available tracks are displayed as a set of tiles along the left right of the main panel. To turn a track on or off, click the arrow in front of the track title from the column on the right.
The ‘Navigation Panel’ runs along the top of the main panel, it includes arrows to move left and right, and two levels of zooming[6]. The dropdown box is used to select the group
(scaffold) for annotation, and the text box is used to manually enter its coordinates.
STEP 6: You can see the different genes and you can check different features.
STEP 7: Click on BLAST.
- 18 -
4.3 BLAST
In the BLAST Tool, select the target genome in the target genome selection reign. The
next section consists of the BLAST parameters; it consists of Type, Color Blast Hits,
Parameters and Nucleotide specific parameters[4]. In the next section, the FASTA
sequence is pasted and then the BLAST is run generating a blast table database and the
blasting sequence generation against the genome.
STEP 8: Enter the FASTA sequence and run the BLAST.
- 19 -
STEP 9: CoGe BLAST run completed.
STEP 10: BLAST output screen.
- 20 -
4.4 Download Data
The FASTA File is available for download.
STEP 11: Click Download.
- 21 -
STEP 12: You can download the FASTA file here.
STEP 13: Click on Synteny.
- 22 -
4.5 Synteny
Synteny describes the physical colocalization of genetic loci on the same chromosome within an individual or species[5].
STEP 14: Select any one comparison.
STEP 15: A comparison between the two genomes can be studied here.
- 23 -
- 24 -
5. Implementation and Analysis
5.1 Model-View-Controller Structure
This project is developed using PHP i.e., Hypertext Preprocessor, using Codeigniter framework. PHP is an open source server-side scripting language that is mainly used for
web development and can be embedded into HTML.
Codeigniter is a framework based on the concept of Model-View-Controller. MVC is a software architectural pattern and it divides the application into three separate components, i.e. model view and controller. Model - logical structure of data in a software application.
This object model does not contain any information about the user interface. View - which is a collection of classes representing the elements in the user interface (all the things the user can see and respond to on the screen, such as buttons, display boxes, and so forth).
Controller - which represents the classes connecting the model and the view, and is used to communicate between classes in the model and view.
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Figure 9 Example of MVC (Web Portal) As shown in Figure 5, the web portal files are organized in the “application” directory as follows:
• The home page of the portal was implemented in “first.php”.
• The “controllers” folder contains all the controller files.
• The “views” folder contains all the view files.
• fig. 4, file directory (Web Portal)
In this project, we have a controller for each page that we load. No Models were implemented in this project as the CoGe database was used. Each tool has a Controller file that loads a view, for example, the JBrowse tool of each species has a controller file, e.g.,
Emiliania huxleyi controller, “JB1.php” loads the view “em.php” that contains the IFrame for the JBrowse tool. Similarly, every page view is loaded from its view.
For Blast tool, controller files are, “B1”, “B2” and “B3” and the corresponding view files are, “Blast1”, “Blast2” and “Blast3”.
- 26 -
For synteny tool, controller files are, “S1”, “S2” and “S3” and the corresponding view files are, “sy1”, “sy2” and “sy3”.
For data downloading, controller files are, “Dw1”, “Dw2” and “Dw3” and the corresponding view files are, “down1”, “down2” and “down3”.
Files, “one.php”, “two.php” and “three.php” are the Controller files of the information of the three genome pages. With the corresponding view, “page1.php”, “page2.php” and
“page3.php”.
Figure 10 file directory (Web Portal) The Model-View-Controller files for this web portal are in the folder “Model”,” View”
and” Controller”. To add any other tool to the web portal, then new controller file in the
“Controller” folder will be needed, which will make the call to a view that needs to be
created in the “View” folder. The view file will contain the IFrame for the new tool that
needs to be added. Let’s take an example, to add a new tool, First, create a new controller
- 27 - and add the link to the page where you want to call this tool. Second, create a view that would contain the IFrame file and the view page of the new tool. Third, call the view from the controller.
In case of a new Genome that needs to be added in the web portal, first its genome and additional annotation data are to be uploaded to the CoGe database, which assigns it a unique genome ID. Then controller files of various tools should be created, which will make calls to the corresponding views files, for JBrowse, BLAST, Download and Synteny.
Let’s take an example, to add a new genome,
First, create a controller like “one.php” that will be called from the home page view.
class one extends CI_Controller { public function index() { $this->load->view('page1.php'); } }
Second, create a view like “em.php” for the new Genome page. Third, In the view of the
genome page, call controllers for each of the tools that needs to be used for that genome,
like “Jb1”, “B1”, “S1” and “Dw1”.
Fourth, create a view for each of the tools to be used and call it from the controller like,
“em1”, “blast1”, “sy1” and “down1”.
5.2 Embedding of CoGe Tools
To implement various tools into the website PHP concept of IFrames has been used.
IFrames is an HTML tag that is used to insert the required content into your web page. It is known to be configured with a scrollbar of its own, irrespective of the scrollbar of the entire page, even though it behaves like an inline image.
Tools like JBrowse, BLAST and Synteny have been embedded into our website using the
concept of IFrames.
IFrame for JBrowse:
IFrame for BLAST:
IFrame for Synteny:
- 29 -
In the above IFrames, the “src” contains the URL of the destination of the tool that has been embedded. The “style” contains the dimensions of the tool that is being embedded
i.e., the width and the height. The “gid” is the id of the genome from CoGe.
5.3 Other Implementation Issues
Some of the front-end development languages that have been used in developing the look and design of our website are HTML5, CSS, Bootstrap and JavaScript. Using these, the
layout of the page and the colors scheme has been designed.
HTML is a markup language that is used to structure the content in the web page. For this
website, the fifth version of HTML is used i.e., HTML5. HTML5 has been used for the
entire layout of the page.
Cascading Style Sheets i.e., CSS is a style sheet language that is used to present a document
that is written in a markup language. Following CSS files were used for the styling that
includes the design and the colors of the web portal. Here is a sample code of the css files.
JavaScript is a client-side scripting language that is written on an HTML page. Whenever any user requests for an HTML page with JavaScript code in it, the script is sent to the browser. This is used to load the IFrames as well as pulling data from CoGe.
Bootstrap is one of the most popular frameworks for HTML5, CSS and JavaScript for developing a responsive website. Bootstrap is used for the implementation of google search bar in the web portal.
- 31 -
6. Conclusion
This website will help in research purpose as the much-needed tools required for the
research of the three genomes i.e., Emiliania huxleyi, Gephyrocapsa oceanica and isochrysisgalbana. are provided in one portal, which makes it easier compared to going on different sites and using different software to do the same task. Using CoGe as the data source is helpful as the data is stored on their server and one does not need to manage the data locally. When required one can access it through our portal and make use of it.
Currently, there are several Universities possessing different portals for this purpose, so
forth the incorporation of this portal not only serves as a great add on to California State
University San Marcos’s Science department, but also it provides an effective platform for
present and future research.
In the future, more tools like Gene Sorter, Genome Graphs, etc. from the UCSC genome
web portal and GEvo tool from CoGe may be added as desired that could help towards the
research. The process of logging into CoGe to access the data and tools can be removed
once the data has been made public. From the design point of view, AngularJS can be used
to make the website responsive. Further, designing new images for the website purpose
would be a good addition, the DNA sequence and the three genomes.
- 32 -
7. References
1. Young, J. R. (n.d.). Emiliania huxleyiand other coccolithophores. Palaeontology
Department, The Natural History Museum, London. [Cited: June 25, 2015].
Retrieved from protozoa.uga.edu/portal/coccolithophores.html
2. Ehux “Tree of Life” alga sequenced. (June 13, 2013). [Cited: June 25, 2015].
Retrieved from algaeindustrymagazine.com/ehux-tree-of-life-alga-sequenced/
3. CoGe basics from,
genomevolution.org/coge/
4. CoGe BLAST tool from,
genomevolution.org/coge/CoGeBlast.pl
5. CoGe Synteny tool from,
genomevolution.org/coge/SynMap.pl
6. JBrowse tool basics from,
jbrowse.org/
7. JBrowse tool basics from,
gmod.org/wiki/JBrowse
8. Emiliania huxleyi. (n.d.). In Wikipedia. [Cited: June 28, 2015]. Retrieved from
en.wikipedia.org/wiki/Emiliania_huxleyi
9. JBrowse implementation explained,
genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0924-1
- 33 -
10. Comparative genomics with maize and other grasses: from genes to genomes. James
C. Schnable1 and Eric Lyons2.
11. CoGe Pedia with required information about CoGe,
genomevolution.org/wiki/index.php/Linking_to_GEvo
12. Similar to our website for the ideas,
genome.ucsc.edu/
13. Video explanation of CoGe,
genomevolution.org/wiki/index.php/Main_Page
14. VISAT
genome.lbl.gov/vista/index.shtml
15. OMIC
omictools.com/
16. Morphological and Phylogenetic Characterization of New Gephyrocapsa Isolates
Suggests Introgressive Hybridization in the Emiliania/Gephyrocapsa Complex.
Bendif, E. M., & Young, J. (2014). On the ultrastructure of Gephyrocapsa oceanica
(Haptophyta) life stages. Cryptogamie, Algologie, 35(4), 379-388.
17. Jin, P., Gao, K., & Beardall, J. (2013). Evolutionary responses of a coccolithophorid
Gephyrocapsa oceanica to ocean acidification. Evolution, 67(7), 1869-1878.
18. Bendif, E. M., Probert, I., Carmichael, M., Romac, S., Hagino, K., & Vargas, C.
(2014). Genetic delineation between and within the widespread coccolithophore
morpho‐species Emiliania huxleyi and Gephyroc apsa oceanica
(Haptophyta). Journal of phycology, 50(1), 140-148.
- 34 -
19. Bendif, E. M., & Young, J. (2014). On the ultrastructure of Gephyrocapsa oceanica
(Haptophyta) life stages. Cryptogamie.
20. Liu, C. P., & Lin, L. P. (2001). Ultrastructural study and lipid formation of Isochrysis sp.
CCMP1324. Botanical Bulletin of Academia Sinica, 42.
21. Eltgroth, M. L., Watwood, R. L., & Wolfe, G. V. (2005). Production and cellular
localization of neutral long‐chain lipids in the haptophyte algae Isochrysis galbana
and Emiliania huxleyi. Journal of Phycology, 41(5), 1000-1009.
7.1 Appendix
Folder Content Upload This folder contains all the images being used in the website. Application This folder consists of all the model, view and controllers: • Config • Model • Controller • Views Controller This folder consists of files that load the views. Views This folder consists of all the HTML files that make the website.
Controller Content Files Welcome.php This file loads the “First.php” home page. One.php This file loads the information page of Emiliania huxleyi. “Page1.php” JB1.php This file loads the JBrowse toolpage of Emiliania huxleyi. “Em.php” Bl1.php This file loads the BLAST tool page of Emiliania huxleyi. “Blast1.php” Dw1.php This file loads the Download page of Emiliania huxleyi. “Down1.php” S1.php This file loads the Synteny tool page of Emiliania huxleyi. “Sy1.php”
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Controller Content Files S11.php This file loads one of the Synteny comparison page of Emiliania huxleyi. “sy11.php” S12.php This file loads one of the Synteny comparison page of Emiliania huxleyi. “sy12.php” Two.php This file loads the information page of Gephyrocapsa oceanica. “Page2.php” JB2.php This file loads the JBrowse tool page of Gephyrocapsa oceanica. “go.php” Bl2.php This file loads the BLAST tool page of Gephyrocapsa oceanica. “Blast2.php” Dw2.php This file loads the Download page of Gephyrocapsa oceanica. “Down1.php” S2.php This file loads the Synteny tool page of Gephyrocapsa oceanica. “Sy1.php” S21.php This file loads one of the Synteny comparison page of Gephyrocapsa oceanica. “sy21.php” S22.php This file loads one of the Synteny comparison page of Gephyrocapsa oceanica. “sy22.php” Three.php This file loads the information page of isochrysisgalbana. “Page3.php” JB3.php This file loads the JBrowse tool page of isochrysisgalbana. “ig.php” Bl3.php This file loads the BLAST tool page of isochrysisgalbana. “Blast3.php” Dw3.php This file loads the Download page of isochrysisgalbana. “Down3.php” S3.php This file loads the Synteny tool page of isochrysisgalbana. “Sy3.php” S31.php This file loads one of the Synteny comparison page of isochrysisgalbana. “sy31.php” S32.php This file loads one of the Synteny comparison page of isochrysisgalbana. “sy32.php”
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View File Content First.php This is the view of the home page of the website. Page1.php This is the view of the information page of Emiliania huxleyi, from here we can access all other tools. Em.php This is the view of the JBrrowse tool of Emiliania huxleyi. Blast1.php This is the view of the BLAST tool of Emiliania huxleyi. Down1.php This is the view of the Emiliania huxleyipage from where we can download the FASTA file. Sy1.php This is the view of the synteny, where there are two comparison files. Sy11.php This is the view of the Synteny with one of the two comparison files. Sy12.php This is the view of the Synteny with one of the two comparison files. Page2.php This is the view of the information page ofGephyrocapsa oceanica, from here we can access all other tools. go.php This is the view of the JBrrowse tool of Gephyrocapsa oceanica. Blast2.php This is the view of the BLAST tool of Gephyrocapsa oceanica. Down2.php This is the view of the Gephyrocapsa oceanicapage from where we can download the FASTA file. Sy2.php This is the view of the synteny, where there are two comparison files. Sy21.php This is the view of the Synteny with one of the two comparison files. Sy22.php This is the view of the Synteny with one of the two comparison files. Page3.php This is the view of the information page of isochrysisgalbana, from here we can access all other tools. ig.php This is the view of the JBrrowse tool of isochrysisgalbana. Blast3.php This is the view of the BLAST tool of isochrysisgalbana. Down3.php This is the view of the isochrysisgalbanapage from where we can download the FASTA file. Sy3.php This is the view of the synteny, where there are two comparison files. Sy31.php This is the view of the Synteny with one of the two comparison files.
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View File Content Sy32.php This is the view of the Synteny with one of the two comparison files.
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