Of course, we ( @axeljanssen.bsky.social) setup a genome browser with a track with sgRNA target sites for easy target validation and gene hunting

We have done it, and we’ve used 25% LB (pmc.ncbi.nlm.nih.gov/articles/PMC...), which we got from another paper (journals.asm.org/doi/10.1128/...).

What other methods did you run into? Did you plan on using another medium?

I'm by no means an expert, but I've used it a fair number of times for some analyses. I'd happy to help where I can. Can you let me know what problems you are experiencing?

Again, thanks to all co-authors for their work on this as well, and other Veening lab members for their continued feedback and bug reports.

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!

These genomes were all sequenced using long-read sequencing techniques (either PacBio or Nanopore sequencing), and we provide the genome methylaton, and genome annotations. Their genomes sequences are available on the NCBI as well!

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.