We have now also added the ability to view pair-wise genome alignments to PneumoBrowse2.

Find this option in the "Linear Synteny" or "Dotplot" alignments views (bottom), or in separate data tracks (per genome).

Thanks for the excellent reviewer comments on this.

Thanks to co-authors Paddy Gibson, Afonso Bravo, Vincent de Bakker, Jelle Slager, and @jwveening.bsky.social for all their hard work, other members of the Veening lab for input and feedback, and Doran Pauka for his support. Feedback is always welcome



We hope you enjoy!

For each gene, we also provide direct links to other databases, such as PneumoWiki, the NCBI, UniProt, PaperBLAST, AlphaFold, and Foldseek, to allow further discovery of biological functions by end-users!

By upgrading to JBrowse 2, we could add other genomes. We added the genomes of 18 other phylogenetically diverse S. pneumoniae strains (orange), including commonly used strains in laboratories such as TIGR4, BHN418, and EF3030, but also Pneumococcal Molecular Epidemiology Network reference strains.

PneumoBrowse 2 has had several major upgrades. We have completely rebuilt it in JBrowse 2, further curated the already detailed manual curration of the S. pneumoniae D39V genome, and added 18 other phylogenetically S. pneumoniae genomes, including TIGR4, and much, much more!

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