Phaeoexplorer web portal

The Phaeoexplorer database for marine brown algae is available at https://phaeoexplorer.sb-roscoff.fr.

General

The Phaeoexplorer website contains information and resources on the different species concerned by the project. The Phaeoexplorer is an ongoing project, and the genome data is not yet publicly available.

Meaning of the icons

The website uses a system of icons to display particular information about an organism. When you hover on these icons, the information is displayed as a text box:

Sequencing types : the nature of the sequencing(s) made for the species (Illumina, Nanopore, PacBio, ...)
Genome assembly score : a rating of the quality of the genome assembly, ranges from 1 star (draft genome) to 3 stars (near chromosome scale assembly)
Best assembly : Whether the organism has the best assembly for the species or not

top menu

The top header menu can be used to navigate the different pages of the website.

A search function is available in the search box at the top right of the header menu You can search for a substring of your favorite organism.

For example, for a search with the string ecto: example search results

Home page

Browse taxonomy

The home page shows the taxonomy tree of the species referenced on the website. This taxonomy has a search function allowing easy access to a particular species. Clicking on one of the leaf nodes of the taxonomy takes the user to the organism page of this species.

taxonomy tree taxonomy tree search

Browse pictures

The home page also contains three sections of species, where only the strains with the best assembly for the species are displayed:

Phaeoexplorer genomes: contains species for which GFF files are available
Upcoming Phaeoexplorer genomes: contains species for which GFF files are not yet available
Published brown algal genomes: contains public species that have not been sequenced by the Phaeoexplorer project. These public organisms pages are accessible to everyone.

By clicking on a photo, you can access to the organism page, with restricted access for unpublished data. (cf. Organism pages)

phaeoexplorer genomes

upcoming phaeoexplorer genomes

public genomes

"All strains" page

This page displays all organisms included in the Phaeoexplorer website, and not only those with the best assembly (as opposed to the home page). Three sections are vailable, as on the home page (cf. Browse pictures)

Organism pages

Restricted access for unpublished data

A dedicated web page exists for every species of the Phaeoexplorer project.

These pages are currently only accessible to members of the Phaeoexplorer consortium. Only the public organisms have unrestricted access.

A same species can have different strains/sex assemblies, in which case a page is available for each strain/sex assembly of the species. The best assembly for the species is indicated using the icon preceding the organism name.

Description

A small header part shows the name of the organism, its assembly score if any, and the links to some available external ressources (NCBI, AlgaeBase, WoRMS, genome browser, ...)

The Description box contains the genus name, species name, strain name and sex of the organism, as well as one or more picture(s) for this organism

organism description

Resources

This box contains the resources available for the species:

The data archive: a tar.gz file that contains all data available for the species (genome, annotation, proteome, de novo transcriptome, ...).
A link to the genome browser (JBrowse)
A link to the genome database (Tripal pages) allowing the user to search and browse specific mRNAs or proteins among other things (cf. Tripal documentation)
Links to external databases: NCBI, AlgaeBase, WoRMS, Roscoff Culture Collection (RCC), ...

organism resources

Assembly, annotation and BUSCO metrics

The Assembly metrics box displays different metrics for the organism assembly.

The Annotation metrics box displays different metrics for the organism annotation.

The BUSCO metrics box displays BUSCO metrics for the organism.

organism metrics

Additional genome assemblies

This box contains links to other strains/sex pages available for the species, if any.

Download page

Restricted access

This page of the website lists all available data generated by the project as downloadable tar.gz archives:

"All" archives: each archive contains a specific type of data (all genomes, all GFF files, all transcriptomes, all proteomes, ... ) of all species
Individual archives: each archive contains all types of data generated for all strains of a single species (genome, GFF file, transcriptome, proteome, ...)

Summary table page