Abstract
BackgroundPhylogenetic information inferred from the study of homologous genes helps us to understand the evolution of genes and gene families, including the identification of ancestral gene duplication events as well as regions under positive or purifying selection within lineages. Gene family and orthogroup characterization enables the identification of syntenic blocks, which can then be visualized with various tools. Unfortunately, currently available tools display only an overview of syntenic regions as a whole, limited to the gene level, and none provide further details about structural changes within genes, such as the conservation of ancestral exon boundaries amongst multiple genomes.FindingsWe present Aequatus, an open-source web-based tool that provides an in-depth view of gene structure across gene families, with various options to render and filter visualizations. It relies on precalculated alignment and gene feature information typically held in, but not limited to, the Ensembl Compara and Core databases. We also offer Aequatus.js, a reusable JavaScript module that fulfills the visualization aspects of Aequatus, available within the Galaxy web platform as a visualization plug-in, which can be used to visualize gene trees generated by the GeneSeqToFamily workflow.
Highlights
Sequence conservation across populations or species can be investigated at multiple levels from single nucleotides, to discrete sequences, genes, genomic blocks, and chromosomes
The Ensembl GeneTrees pipeline [11], a computational workflow developed by the EMBL-EBI Ensembl Compara team, produces familial relationships based on clustering, multiple sequence alignment (MSA), and phylogenetic tree inference
Main gene trees view The gene tree view comprises a phylogenetic tree on the left, built from GeneTree information stored in a Ensembl Compara database [11]
Summary
Sequence conservation across populations or species can be investigated at multiple levels from single nucleotides, to discrete sequences (e.g. transcription factor binding sites, exons, introns), genes, genomic blocks, and chromosomes. The Ensembl Core databases store gene feature information and other genomic annotations at the species level. Currently available tools display only an overview of syntenic regions as a whole, limited to the gene level, and none provide further details about structural changes within genes, such as the conservation of ancestral exon boundaries amongst multiple genomes. Findings: We present Aequatus, an open-source web-based tool that provides an in-depth view of gene structure across gene families, with various options to render and filter visualizations. It relies on precalculated alignment and gene feature information typically held in, but not limited to, the Ensembl Compara and Core databases. We offer Aequatus.js, a reusable JavaScript module that fulfills the visualization aspects of Aequatus, available within the Galaxy web platform as a visualization plug-in, which can be used to visualize gene trees generated by the GeneSeqToFamily workflow
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