Aequatus Browser, an open-source web-based tool developed at TGAC to visualise homologous gene structures among differing species or subtypes of a common.

• Aequatus Browser, an open-source web-based tool developed at TGAC to visualise homologous gene structures among differing species or subtypes of a common species. Aequatus works on top of the Ensembl Compara and Core database schema.

• Aequatus uses precalculated gene family information and genomic alignments data in the form of CIGAR strings, from Ensembl Compara, and cross-references these sequences to Ensembl Core databases for each species to gather genomic feature information via stable_ids. Aequatus then processes the comparative and feature data to provide a visual representation of the phylogenetic and structural relationships among the set of chosen species.

• The ultimate goal of the Aequatus Browser is to provide a unique and informative way to render and explore complex relationships between genes from various species at a level that has so far been unrealised.

Aequatus

Controls

Search Genomes

Chromosomes

Navigation PanelGene Members

Homologous View

Overview

Main window of Aequatus contains various components to search genes, select gene and species and control homologous view, which are annotated in the image below:

Aequatus BrowserHomologous View

Insertions

Deletions

Shared Exon

Shared exons within or between species are shown with same colour

Insertsions in shared exons are shown with black blocks and deletions with carat(v) on top

Visualising homologous genes with phylogenetic tree.

Search Term

Previous Search• Retrieve results by just clicking on it

Result matching search term• Showing Gene location, description, stable_id, and direct link to the

homologous gene view

Search

Toggle visuals of match, insertions, deletions, and UTRs from homologous view

Toggle label between stable_id and gene info

Toggle between actual intron size or fixed length intron view

Settings

Legends

Showing event happened in evolution with colour coded nodes

RestAPI

• Aequatus has a hard-link REST API for easy access to genes of interest, making it simple to share information and visualisations with collaborators.

• Example– http://…/index.jsp?query=AT1G01710.1

• This will directly load homologous view of the gene– http://…/index.jsp?search=AT1G0171

• This will search for the term in databases and show results– http://…/index.jsp?ref=arabidopsis_thaliana&chr=4

• This will directly jump to the species and reference chromosome

• For any kind of enquiry about Aequatus please contact us:– Anil.Thanki@tgac.ac.uk– Robert.Davey@tgac.ac.uk

Aequatus contact