Aequatus Browser, an open-source web-based tool developed at Earlhan Institute 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.
Project Website: http://aequatus.earlham.ac.uk/
Source Code: https://github.com/tgac/aequatus-browser
License: GPL V3
When you start Aequatus it starts with a blank screen with chromosomal view on top and Gene view.
Two option to start with:
For the purpose of changing reference genome. Reference Genome can be set from the dropdown on top-right corner.
Select Chromosome:For the purpose of selecting reference chromosome. Select on any of the chromosome karyotype from window.
Select Reference Gene:
For the purpose of selecting reference gene. Select on any of the gene from Gene view or for gene of interest search for gene with keyword.
Here Aequatus visualises Homologous genes with phylogenetic tree.
Homologous gene view shows shared exons with smae colour in all genes structure. insertion
Homologous geneview shows shared exons insertion and deletions.
Here we have various controls to change settings of Aequatus like, toggle view, search, change label etc.
with this control chromosome view can be show or hide, to get more area to display homologous view.
With chromosome view
Without chromosome view
Aequatus has few options to controls to alter visuals of homologous view.
In Aequatus search can be done from either of the search boxes, any keywords can be used for search like Accession no., stable id, functionality, etc.
Aequatus has a hard-link REST API for easy access to genes of interest, making it simple to share information and visualisations with collaborators.
Changing Reference Gene
In Aequatus main homologous gene view, Reference gene is the main selected gene, on which other genes alignments are mapped on, Any other gene from view can be used as reference gene by clicking on it and click on tree icon in pop-up.
How to setup
Table of content
Aequatus Browser requires
Installing and running Aequatus Browser
You will need Maven 2.2.1 to build Aequatus Browser (*NOTE Not Maven 3!*). Once you have grabbed the code and installed Maven, in the root of the project (you should see a pom.xml file and module directories like browser-web and core etc) call:
It will generate a aequatus-browser.war file copy it to Apache Tomcat webapps and start the Tomcat server.
Aequatus Browser should be running at http://<server-path>/aequatus-browser
Aequatus Browser property file contains many features those can be changed in browser straight away
Standard featuresbrowser.title = Demo