Annotates transcripts in a Genome object with metabolic functions using OrthoFinder.
This App takes a Genome object as the input and uses OrthoFinder to cluster transcripts with Arabidopsis enzymes curated in PlantSEED. It also annotates the protein-coding genes with metabolic functions and provides the annotated Genome object as an output. Each of the Arabidopsis enzymes are used as the initial member of each cluster, and every transcript in the selected genome is placed within the same cluster if it meets two main criteria: (i) the sequence identity of the transcript-enzyme pair is higher than the other transcript-enzyme pairs and (ii) the sequence identity of the transcript-enzyme pair meets the selected threshold. More details on this selection process can be found in the publications. Once placed in a cluster, the metabolic function of the enzyme is propagated to the transcripts in the same cluster. The annotations are linked to biochemical reactions, and researchers may use the Reconstruct Plant Metabolism App to follow up and build a working model of plant primary metabolism.
- Emms DM, Kelly S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 2015;16. doi:10.1186/s13059-015-0721-2 , https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4531804/
- OrthoFinder GitHub source: , https://github.com/davidemms/OrthoFinder
- PlantSEED Github source: , https://github.com/ModelSEED/PlantSEED/
Module Commit: 3716d510f5eac599e29c87540f6b2db7dc81c8c8