Annotating transcripts with metabolic functions
This app is released in conjunction with PlantSEED v2 (see publications). It integrates the set of signature k-mers that were trained as part of the PlantSEED v2 project, wherein every k-mer is unique, and associated with a single metabolic function. The app will scan the protein sequences for hits and assign the function accordingly. The annotations are linked to biochemical reactions, and researchers may use the "Build Metabolic Model" app. Please note: we did not integrate protein localization data when training the k-mers and this impacts compartmentalization of GPRs in our metabolic reconstructions. For more reliably compartmentalized GPRs, you may instead annotate your genome using the "Annotate Plant Enzymes with OrthoFinder" app.
- Seaver SMD, Lerma-Ortiz C, Conrad N, Mikaili A, Sreedasyam A, Hanson AD, et al. PlantSEED enables automated annotation and reconstruction of plant primary metabolism with improved compartmentalization and comparative consistency. Plant J. 2018;95: 1102 1113. doi:10.1111/tpj.14003 , https://www.ncbi.nlm.nih.gov/pubmed/29924895
- Seaver SMD, Gerdes S, Frelin O, Lerma-Ortiz C, Bradbury LMT, Zallot R, et al. High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource. Proc Natl Acad Sci USA. 2014;111: 9645 9650. doi:10.1073/pnas.1401329111 , https://www.ncbi.nlm.nih.gov/pubmed/24927599
- GitHub source: , https://github.com/ModelSEED/PlantSEED/
Module Commit: 45b3934211eca408bf3e083b8f4a6ec29843cd6a