Also, catabolic gene cluster absence/presence profiles were shown to be strongly predictive of rhizosphere competence, even more so than a dataset of experimental assays of catabolic potential. 4/4

Running rhizoSMASH on a large collection of plant- and soil-associated genomes enabled charting the first map of root-associated catabolic functions across key plant-associated microbial taxa. 3/4

Similar as for antiSMASH and later gutSMASH, Yuze curated a set of profile HMMs and detection rules to reliably identify these gene clusters, guided by sequence similarity network analysis to distinguish true positives from false positives accurately. 2/4

... and expression (anti-)correlations of biosynthetic gene clusters highlight positive and negative responses to antibiotic production (related to stress response, siderophores, redox balance).

Coexpression networks of primary metabolic modules highlight both competition and cross-feeding...

At the same time, for mid-size datasets (most frequent use case), BiG-SCAPE v2 approaches the speed of BiG-SLiCE. For larger datasets, BiG-SCAPE has become more resource-efficient, which now allowed us to analyse >250k BGCs (the antiSMASH database) with it in just a few days on a compute server.

Benchmarking on several different types of ground truth datasets shows the increases in accuracy, with BiG-SLiCE v2 often matching BiG-SCAPE v1 accuracy, and BiG-SCAPE v2 combining its speed increase with a small but notable accuracy gain as well.

BiG-SCAPE was completely rewritten from scratch over the past few years, and now features new alignment modes, a more prominent query mode (which allows you to search genomes from a single BGC query) and more scalable interactive visualizations and data selection/filtering.

At our NPlinker symposium, co-chair @jjjvanderhooft.bsky.social illustrates pattern mining using an example from the Alhambra.

Looking forward to co-hosting the festive symposium on integrative omics in Omnia @w-u-r.bsky.social this afternoon together with @jjjvanderhooft.bsky.social . Celebrating 10 years of computational genome mining and 5 years of computational metabolome mining in Wageningen!

It was great to host @jlsteenwyk.bsky.social in Wageningen for a seminar today. Exciting discussions about orthology predictions, bioinformatic software/tool development and applications on interesting biological and biochemical problems...

INVITATION We are starting a new round of online community annotathons to populate v4.0 of the MIBiG repository with high-quality data. If you have relevant expertise in natural product genomics or chemistry, please participate! Please register here: forms.gle/LJR9uRTCyLg7...