CusProSe: a customizable protein annotation software with an application to the prediction of fungal secondary metabolism genes - I2BC Accéder directement au contenu
Article Dans Une Revue Scientific Reports Année : 2023

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

Résumé

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.
Fichier principal
Vignette du fichier
Leonor_Oliveira_article.pdf (2.94 Mo) Télécharger le fichier
Origine : Fichiers éditeurs autorisés sur une archive ouverte
licence : CC BY - Paternité

Dates et versions

hal-03975487 , version 1 (21-11-2023)

Licence

Paternité

Identifiants

Citer

Leonor Oliveira, Nicolas Chevrollier, Jean-Félix Dallery, Richard O'Connell, Marc-Henri Lebrun, et al.. CusProSe: a customizable protein annotation software with an application to the prediction of fungal secondary metabolism genes. Scientific Reports, 2023, 13 (1), pp.1-13. ⟨10.1038/s41598-023-27813-y⟩. ⟨hal-03975487⟩
94 Consultations
5 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More