CusProSe: a customizable protein annotation software with an application to the prediction of fungal secondary metabolism genes

We report here a new application, CustomProteinSearch (CusProSe), whose purpose is to help users to search for proteins of interest based on their domain composition. The application is customizable. It consists of two independent tools, IterHMMBuild and ProSeCDA. IterHMMBuild allows the iterative construction of Hidden Markov Model (HMM) profiles for conserved domains of selected protein sequences, while ProSeCDA scans a proteome of interest against an HMM profile database, and annotates identified proteins using user-defined rules. CusProSe was successfully used to identify, in fungal genomes, genes encoding key enzyme families involved in secondary metabolism, such as polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), hybrid PKS-NRPS and dimethylallyl tryptophan synthases (DMATS), as well as to characterize distinct terpene synthases (TS) sub-families. The highly configurable characteristics of this application makes it a generic tool, which allows the user to refine the function of predicted proteins, to extend detection to new enzymes families, and may also be applied to biological systems other than fungi and to other proteins than those involved in secondary metabolism.

Automated summary

In this article, we introduce a new application called CustomProteinSearch (CusProSe), which is designed to help users search for proteins based on their domain composition. The application consists of two customizable tools, IterHMMBuild and ProSeCDA. IterHMMBuild allows for the iterative construction of Hidden Markov Model (HMM) profiles for specific protein sequences, while ProSeCDA scans a proteome using an HMM profile database and annotates identified proteins using user-defined rules. We successfully used CusProSe to identify genes encoding key enzyme families involved in secondary metabolism in fungal genomes, as well as characterize different sub-families of terpene synthases.