Comparative genomics is a well proven method that allows researchers to delve into the genetic blueprints of organisms, deciphering their similarities, differences, and evolutionary histories. It's a vital tool for understanding genomes and genes, their expression, function and interaction. In this field, the EDGAR platform, created by Jochen Blom and his team, is one of the most established options.
What is EDGAR?
EDGAR, is a robust platform tailored to streamline the process of comparing microbial genomes. It's build to handle this compute intensive task for hundreds of organisms, ensuring that researches can perform their analyses without requiring extensive local computational resources.
At the heart of EDGAR lies the calculation of orthology relational information between sets of genomes on species, genus or even family level. Using BLAST score ratios, EDGAR pinpoints conserved and divergent regions within sequence sets. This process is crucial for identifying genes and genomic regions that may play vital roles in an organism's biology.
A Database-Resource and multifaceted toolkit
EDGAR relies on a comprehensive database of precomputed results for a diverse range of genomes, currently curating ~750 public projects with more than 24,000 organisms for users around the world. For the analysis of unpublished data, a further 1,300 private projects with 60,000 genomes are hosted. This databases enable researchers to rapidly compare a query arbitrary genomes, all without the need to conduct time consuming BLAST searches for each comparison.
In the interactive EDGAR web-interface, users can customise their analyses by selecting specific genomes for comparison, adjusting parameters, and exploring various aspects of their data by using a wide array of features and visualisations.
A key feature of the EDGAR platform is its ability to calculate gene-sets, including the core-, dispensable and singleton genes within an all encompassing pan-genome. These gene-sets shed light on which genes are conserved across species and which are unique to specific lineages.
EDGAR allows researchers to study evolutionary relationships between species using the data derived from the orthology calculations. For every project a phylogenetic tree is constructed based on the complete core genome, the set of genes conserved among all genomes of a project. Genome similarity matrices like AAI/ANI enable users to classify and position their microbes within the tree of life.
In response to user feedback, EDGAR now provides analysis features for functional categories from the respected KEGG, COG and GO databases. The new features provide the ability to interactively explore quantitative functional category annotations for pan-genomic subsets, or to compare the proportions of functional categories between individual strains to gain insight into their diverse metabolic potential.
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In conclusion, EDGAR is a compelling platform that significantly contributes to the field of comparative genomics and phylogenomics. Its efficiency and scalability in orthology calculation, and the feature-rich interactive web interface, make it a powerhouse for microbiologists. By providing easy access to complex genome analyses, EDGAR enables scientists to focus on what truly matters - discovering the mechanisms behind the code of life.
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