MicrobesOnline

The main aim of MicrobesOnline is to provide an easy-to-use resource that integrates a wealth of data from multiple sources.

The development of high-throughput methods for genome sequencing has brought about a wealth of data that requires sophisticated bioinformatics tools for their analysis and interpretation.

[3] Nowadays, numerous tools exist to study genomics sequence data and extract information from different perspectives.

However, the lack of unification of nomenclature and standardised protocols between tools, makes direct comparison between their results very difficult.

[4] Additionally, the user is forced to constantly switch from various websites or software, adjusting the format of their data to fit with individual requirements.

MicrobesOnline was developed with the aim to integrate the capacities of different tools into a unified platform for easy comparison between analysis results, with a focus on prokaryote species and basal eukaryotes.

MicrobesOnline hosts genomic, gene expression and fitness data for a wide range of microbial species.

[6] The homepage of MicrobesOnline is the portal for accessing its functions, which includes six main sections: the top navigation elements, a genome selector, examples of the tutorial based on E.coli K-12, a link to the Genome-Linked Application for Metabolic Maps (GLAMM), website highlights and the “about MicrobesOnline” list.

On the right side of the genome selector, four actions can be applied after selecting genomes: the “find genes” interface searches the gene name in the selected genomes and displays results in the gene list view; the “info” button lists a brief summary of selected genomes in the Summary View; the “GO” button opens a GO Browser called VertiGo which tabulates the number of genes under different GO items; finally, the “pathway” button initiates a pathway browser that illustrates the complete pathways of all organisms in the MicrobesOnline database.

The GO Browser, also known as VertiGo, is used by MicrobesOnline to search and visualise the GO hierarchy, which is a unified verbal system that describes properties of gene products, including cellular components, molecular function and biological process.

MicrobesOnline stores information of gene homology and phylogeny for comparative genomic studies, which can be accessed through two interfaces.

Analyses currently supported include multiple sequence alignments, construction of phylogenetic trees, motif searches and scans, summaries of gene expression profiles and protein-protein interactions.

[39] MicrobesOnline is compatible with other similar platforms of integrated microbe data, such as IMG and RegTransBase, given that standard identifiers of genes are maintained throughout the database.

However, notable efforts have been made by other teams to create comprehensive platforms that largely overlap with the capabilities of MicrobesOnline.

With a similar web interface to MicrobesOnline, the user is capable of toggling between sites via the “switch to” link on the homepage.

An overview of the core components of the MicrobesOnline site
The homepage of MicrobesOnline with six major sections for accessing the database highlighted.
An example of the gene list view
A custom demonstration of the temporary gene cart and the permanent gene cart.
Genes of E.coli K-12 substrain DH10B under the highlighted GO item “cell adhesion”.
The experiment browser as a component of the Expression Data Viewer.
A species tree view in rectangular style
A gene context view, which shows the contexts of genomes beside a gene tree.
The orthology around VIMSS ID 15779 of five given genomes displayed in the Orthology Browser.
The pyruvate metabolism pathway illustrated by the Pathway Browser.
The KEGG pathway map of Rickettsia rickettsii is visualised by GLAMM with a metabolite highlighted.
The layout of Bioinformatics Workbench
A summary of the databases of MicrobesOnline