A knowledge-driven protocol for prediction of proteins of interest with an emphasis on biosynthetic pathways.

ABSTRACT: This protocol describes a stepwise process to identify proteins of interest from a query proteome derived from NGS data. We implemented this protocol on Moringa oleifera transcriptome to identify proteins involved in secondary metabolite and vitamin biosynthesis and ion transport. This knowledge-driven protocol identifies proteins using an integrated approach involving sensitive sequence search and evolutionary relationships. We make use of functionally important residues (FIR) specific for the query protein family identified through its homologous sequences and literature. We screen protein hits based on the clustering with true homologues through phylogenetic tree reconstruction complemented with the FIR mapping. The protocol was validated for the protein hits through qRT-PCR and

SUBMITTER: Joshi AG 

PROVIDER: S-EPMC7528181 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature