Download Aequatus User Guide

Aequatus
• 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.
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:
Search
Chromosomes
Navigation Panel
Gene Members
Controls
Homologous View
Genomes
Aequatus Browser
Homologous
View
Visualising homologous
genes with phylogenetic
tree.
Shared Exon
Shared exons within or
between species are
shown with same colour
Deletions
Insertions
Insertsions in shared
exons are shown with
black blocks and
deletions with carat(v) on
top
Search
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
Settings
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
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
Aequatus contact
• For any kind of enquiry about Aequatus please contact us:
– [email protected]
– [email protected]