Metabolic Pathway Assignment of Plant Genes based on Phylogenetic Profiling-A Feasibility Study.

ABSTRACT: Despite many developed experimental and computational approaches, functional gene annotation remains challenging. With the rapidly growing number of sequenced genomes, the concept of phylogenetic profiling, which predicts functional links between genes that share a common co-occurrence pattern across different genomes, has gained renewed attention as it promises to annotate gene functions based on presence/absence calls alone. We applied phylogenetic profiling to the problem of metabolic pathway assignments of plant genes with a particular focus on secondary metabolism pathways. We determined phylogenetic profiles for 40,960 metabolic pathway enzyme genes with assigned EC numbers from 24 plant species based on sequence and pathway annotation data from KEGG and Ensembl Plants. For gene sequ

SUBMITTER: Weißenborn S 

PROVIDER: S-EPMC5664361 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature