Prediction of protein subplastid localization and origin with PlastoGram.
Sci Rep
; 13(1): 8365, 2023 05 24.
Article
em En
| MEDLINE
| ID: mdl-37225726
ABSTRACT
Due to their complex history, plastids possess proteins encoded in the nuclear and plastid genome. Moreover, these proteins localize to various subplastid compartments. Since protein localization is associated with its function, prediction of subplastid localization is one of the most important steps in plastid protein annotation, providing insight into their potential function. Therefore, we create a novel manually curated data set of plastid proteins and build an ensemble model for prediction of protein subplastid localization. Moreover, we discuss problems associated with the task, e.g. data set sizes and homology reduction. PlastoGram classifies proteins as nuclear- or plastid-encoded and predicts their localization considering envelope, stroma, thylakoid membrane or thylakoid lumen; for the latter, the import pathway is also predicted. We also provide an additional function to differentiate nuclear-encoded inner and outer membrane proteins. PlastoGram is available as a web server at https//biogenies.info/PlastoGram and as an R package at https//github.com/BioGenies/PlastoGram . The code used for described analyses is available at https//github.com/BioGenies/PlastoGram-analysis .
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Genomas de Plastídeos
/
Proteínas de Cloroplastos
Tipo de estudo:
Prognostic_studies
/
Risk_factors_studies
Idioma:
En
Ano de publicação:
2023
Tipo de documento:
Article