Aequatus: An open-source homology browser

Thanki, Anil; Ayling, Sarah; Herrero, Javier; Davey, Robert P.

doi:10.1101/055632

Cited by 2 publications

(3 citation statements)

References 24 publications

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“…Gene Alignment and Family Aggregator (GAFA) GAFA is a Galaxy tool which generates a single SQLite database [15] containing the gene tree and multiple sequence alignment, along with gene features, in order to provide a reusable, persistent data store for visualisation of synteny information with Aequatus [12] . GAFA requires a gene tree file in Newick format [34] , the CIGAR alignment, and gene feature information generated with the GFF3-to-JSON tool, which are then merged into a single SQLite file.…”

Section: Gene Alignment and Family Aggregationmentioning

confidence: 99%

“…It is also possible to develop custom visualisation plugins and easily integrate them into Galaxy. As the output of the GeneSeqToFamily workflow is not conducive to human readability, we also provide a data-to-visualisation plugin based on the Aequatus software [12] . Aequatus.js [13] is a new JavaScript library for the visualisation of homologous genes, which is extracted from the standalone Aequatus tool.…”

Section: Introductionmentioning

confidence: 99%

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GeneSeqToFamily: the Ensembl Compara GeneTrees pipeline as a Galaxy workflow

Thanki

Soranzo

Haerty

et al. 2016

Preprint

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BackgroundGene duplication is a major factor contributing to evolutionary novelty, and the contraction or expansion of gene families has often been associated with morphological, physiological and environmental adaptations. The study of homologous genes helps us to understand the evolution of gene families. It plays a vital role in finding ancestral gene duplication events as well as identifying genes that have diverged from a common ancestor under positive selection. There are various tools available, such as MSOAR, OrthoMCL and HomoloGene, to identify gene families and visualise syntenic information between species, providing an overview of syntenic regions evolution at the family level. Unfortunately, none of them provide information about structural changes within genes, such as the conservation of ancestral exon boundaries amongst multiple genomes. The Ensembl GeneTrees computational pipeline generates gene trees based on coding sequences and provides details about exon conservation, and is used in the Ensembl Compara project to discover gene families.

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Section: Gene Alignment and Family Aggregationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

GeneSeqToFamily: the Ensembl Compara GeneTrees pipeline as a Galaxy workflow

Thanki

Soranzo

Haerty

et al. 2016

Preprint

Self Cite

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“…Of those, the Galaxy Workbench is an open-source web-based software framework that aims to make commandline tools accessible to users without informatic expertise (The Galaxy Community, 2022), and is popular among biologists. Galaxy implements several comparative genomic tools developed by the bioinformatics community (Darling et al, 2010;Thanki et al, 2018). Such a web-based framework provides a simplified way to execute standardized analyses and workflows.…”

Section: Introductionmentioning

confidence: 99%

PlantTribes2: Tools for comparative gene family analysis in plant genomics

et al. 2023

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Plant genome-scale resources are being generated at an increasing rate as sequencing technologies continue to improve and raw data costs continue to fall; however, the cost of downstream analyses remains large. This has resulted in a considerable range of genome assembly and annotation qualities across plant genomes due to their varying sizes, complexity, and the technology used for the assembly and annotation. To effectively work across genomes, researchers increasingly rely on comparative genomic approaches that integrate across plant community resources and data types. Such efforts have aided the genome annotation process and yielded novel insights into the evolutionary history of genomes and gene families, including complex non-model organisms. The essential tools to achieve these insights rely on gene family analysis at a genome-scale, but they are not well integrated for rapid analysis of new data, and the learning curve can be steep. Here we present PlantTribes2, a scalable, easily accessible, highly customizable, and broadly applicable gene family analysis framework with multiple entry points including user provided data. It uses objective classifications of annotated protein sequences from existing, high-quality plant genomes for comparative and evolutionary studies. PlantTribes2 can improve transcript models and then sort them, either genome-scale annotations or individual gene coding sequences, into pre-computed orthologous gene family clusters with rich functional annotation information. Then, for gene families of interest, PlantTribes2 performs downstream analyses and customizable visualizations including, (1) multiple sequence alignment, (2) gene family phylogeny, (3) estimation of synonymous and non-synonymous substitution rates among homologous sequences, and (4) inference of large-scale duplication events. We give examples of PlantTribes2 applications in functional genomic studies of economically important plant families, namely transcriptomics in the weedy Orobanchaceae and a core orthogroup analysis (CROG) in Rosaceae. PlantTribes2 is freely available for use within the main public Galaxy instance and can be downloaded from GitHub or Bioconda. Importantly, PlantTribes2 can be readily adapted for use with genomic and transcriptomic data from any kind of organism.

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Aequatus: An open-source homology browser

Cited by 2 publications

References 24 publications

GeneSeqToFamily: the Ensembl Compara GeneTrees pipeline as a Galaxy workflow

GeneSeqToFamily: the Ensembl Compara GeneTrees pipeline as a Galaxy workflow

PlantTribes2: Tools for comparative gene family analysis in plant genomics

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