OpenGenomeBrowser: a versatile, dataset-independent and scalable web platform for genome data management and comparative genomics

Abstract

Background As the amount of genomic data continues to grow, there is an increasing need for systematic ways to organize, explore, compare, analyze and share this data. Despite this, there is a lack of suitable platforms to meet this need. Results OpenGenomeBrowser is a self-hostable, open-source platform to manage access to genomic data and drastically simplifying comparative genomics analyses. It enables users to interactively generate phylogenetic trees, compare gene loci, browse biochemical pathways, perform gene trait matching, create dot plots, execute BLAST searches, and access the data. It features a flexible user management system, and its modular folder structure enables the organization of genomic data and metadata, and to automate analyses. We tested OpenGenomeBrowser with bacterial, archaeal and yeast genomes. We provide a docker container to make installation and hosting simple. The source code, documentation, tutorials for OpenGenomeBrowser are available at opengenomebrowser.github.io and a demo server is freely accessible at opengenomebrowser.bioinformatics.unibe.ch. Conclusions To our knowledge, OpenGenomeBrowser is the first self-hostable, database-independent comparative genome browser. It drastically simplifies commonly used bioinformatics workflows and enables convenient as well as fast data exploration.

Scoary2: rapid association of phenotypic multi-omics data with microbial pan-genomes

“…Furthermore, the gene loci (Fig. 5 E/F) were compared using OpenGenomeBrowser [ 40 ] via custom URLs as mentioned earlier, revealing that the two genes are indeed adjacent and located in a syntenic gene cluster, one gene away from an L-carnitine CoA transferase ( caiA ). In the isolates which lack the two genes, many of the clusters were seemingly disjoined by transposases and other genes on the cluster were pseudogenized (Fig.…”

Scoary2:Rapid association of phenotypic multi-omics data with microbial pan-genomes

“…A closer look at the gene identifiers suggests that the two genes are adjacent. Furthermore, the gene loci (Figure 4 E/F) were compared using OpenGenomeBrowser [42] via custom URLs as mentioned earlier, revealing that the two genes are indeed adjacent and located in a syntenic gene cluster, one gene away from an L-carnitine CoA transferase (caiA). In the isolates which lack the two genes,many of the clusters were seemingly disjoined by transposases and other genes on the cluster were pseudogenized (Figure 4 E/F).…”

“…If the app is connected to external comparative genomics tools, it becomes easy to study the candidate gene in more detail. In our example, OpenGenomeBrowser [42] enabled us to discover that the two genes most strongly associated with carnitines are located on the same gene cluster and near an L-carnitine CoA transferase, providing more evidence for a causal relationship.…”

“…The gene locus plots (Figure 4) were generated using OpenGenomeBrowser [42], which utilizes DNA Features Viewer [79], and modified using Adobe Illustrator [80].…”

The lactonase BxdA mediates metabolic adaptation of maize root bacteria to benzoxazinoids

“…Two approaches were investigated independently. The first consisted of grouping the genes into orthogroups with OrthoFinder v. 2.3.8 53 and estimating significant associations between the phenotype and orthogroups by applying Fisher’s Exact Test using the gene trait matching tool in OpenGenomeBrowser 58 . In the second approach, a kmer-similarity search strategy was conducted.…”