Help Page


Table of Content

DemaDB is a database for dematiaceous fungi. To learn more about dematiaceous fungi, please visit here.

All the data contained in DemaDB is open for public access, as long as one comply with the Data Usage Policy (will be shown before you navigate the data).

There are a total of 8 projects in DemaDB, all with detailed information and data. Users are able to Search, View the Sequencing Stats, Download, visualize the genome in GBrowse and perform various other operations.

1. Introduction

Hover to "Introduction" button (first from the left) on the top menu. In this section, you can find out more about DemaDB, for example our Focus, Brief Introduction and others.

2. Projects

From the top menu, click on "Projects" (second button from the left) to access this section. This section contains general information and overview about each of the projects.

After that, from the list on Right Hand Side, you can click on any project to view more about it.

For example, if Bipolaris papendorfii UM 226 is selected, a page with all the associated informations and details about it will be shown. On the right hand side of the page, there is a menu with quick links to different sections of informations about the project.

From this menu, you may also download the associated data, or browse the genome in Genome Browser (GBrowse). For more information about GBrowse, refer to section 3.5

3. Fungal Genomes

From the top menu, click on "Fungal Genomes" (third button from the left) to access this section, then read and accept the Policy. This section contains Genomics Information of all the data stored on DemaDB.

Under the header, there are several options in which you can select to view or query the Genomics Data.

3.1 Genome Index

This page lists out all the Genomes available, as well as its status and annotation.

3.2 Assembly Statistics

This page shows the statistics from assembly for each genomes. For example the N50, GC Content etc.

3.3 Gene Models

This page shows the statistics of Gene Models for each genomes. For example the Average Gene Length, number of rRNAs etc.

3.4 Gene Annotation & Classification

This page shows the number of various type of Gene Annotation & Classification found in respective genomes. For example KEGG, GO, InterPro etc.

On the Search box near the top, you could type in keyword to perform pre-filter for all the data.

You could click on the number to show the set of annotation/classification in table form. The figure below shows the page listing out all the KEGG annotation of Bipolaris papendorfii.

3.5 Genome Browser

To understand the basic usage of Genome Browser, please visit GBrowse General Help page.

This page shows the link to Genome Browser for all the available genomes. User has to accept read and accept the Policy before browsing.

The figure below shows the GBrowse page for Bipolaris papendorfii UM 226 genome.

User could freely browse and navigate the different part of the genome and its annotation. As for the features highlighted in red :

  1. Click to select the genome in order to switch to the selected genome.
  2. Click to show more information about the gene.
  3. Hide/Unhide various available data tracks through this subsection.

3.6 Pathway Browser

This page presents the available KEGG pathway for individual genes, should they available.

User could switch between genomes from the panel on left hand side. As for the features highlighted in red :

  1. The number of unique EC Number for the pathway. Click to view each of the EC number.
  2. The number of genes for the pathway. Click to view each of the genes.
  3. Click to view all Pathway for the genome, in summarized form.
  4. Click to view all pathway for the genome.

In the table listings, user could click on the Path ID to show the KEGG Pathway chart in visual form. For example, the figure below shows the table of Unique EC number.

4. Downloads

From the top menu, click on "Downloads" (fourth button from the left) to access this section. For each of the genomes, this section lists the Assembly, Proteins and Nucleotides files available for download.

Note that user have to accept the Data Usage Policy bofore download.