Tools

These methods enabled the discovery of diverse, potent compounds from uncultivated bacteria and poorly studied bacterial lineages.

TransPACT

The external pagetransPACT algorithm (external pageNature Communications) identifies conserved chemical substructures in trans-AT PKS-derived polyketides. We used it to study evolutionary patterns across bacterial genomes and to discover polyketide variants with conserved moieties.

Code at external pageGitHub

transPACT workflow — Workflow of the transPACT application (trans-AT PKS Annotation and Comparison Tool). Adapted from Helfrich et al., Nature Chemical Biology 2021.

TransATor

The TransATor tool (external pageNature Chemical Biology) makes structure predictions for trans-AT PKS-derived polyketides from protein sequences. We applied it for hypothesis-based polyketide discovery and biosynthetic studies.

Free TransATor web application at transator.ethz.ch/trans-AT-PKS/
Code and tutorial at external pageGitHub

TransATor workflow. — TransATor (*trans*-AT PKS polyketide predictor) workflow.

Metaboseek

external pageMetaboseek is a tool to analyze LC/MS data. Molecular features are detected and compared across mutliple samples. Metaboseek was developed by former PhD student Dr. Maximilian Helf at Cornell University (external pageNature Communications).

Free Metaboseek web application at external pagemetaboseek.com
Code at external pageGitHub