PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes
Pourquoi ce travail est-il dans la base ?
Une base qui oublie comment elle a trouvé un travail ne peut pas être vérifiée. Voici les voies qui ont admis celui-ci.
Résumé
MOTIVATION: PSORTb has remained the most precise bacterial protein subcellular localization (SCL) predictor since it was first made available in 2003. However, the recall needs to be improved and no accurate SCL predictors yet make predictions for archaea, nor differentiate important localization subcategories, such as proteins targeted to a host cell or bacterial hyperstructures/organelles. Such improvements should preferably be encompassed in a freely available web-based predictor that can also be used as a standalone program. RESULTS: We developed PSORTb version 3.0 with improved recall, higher proteome-scale prediction coverage, and new refined localization subcategories. It is the first SCL predictor specifically geared for all prokaryotes, including archaea and bacteria with atypical membrane/cell wall topologies. It features an improved standalone program, with a new batch results delivery system complementing its web interface. We evaluated the most accurate SCL predictors using 5-fold cross validation plus we performed an independent proteomics analysis, showing that PSORTb 3.0 is the most accurate but can benefit from being complemented by Proteome Analyst predictions. AVAILABILITY: http://www.psort.org/psortb (download open source software or use the web interface). CONTACT: psort-mail@sfu.ca SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Récupéré en direct depuis OpenAlex et désinversé. Les résumés ne sont pas conservés dans cette base de données : les index inversés représentent 8,6 Go des 9,3 Go de texte de la base, et le serveur dispose de 13 Go libres.
La notice
- Revue
- Bioinformatics
- Thématique
- Machine Learning in Bioinformatics
- Domaine
- Biochemistry, Genetics and Molecular Biology
- Établissements canadiens
- Simon Fraser UniversityUniversity of British Columbia
- Organismes subventionnaires
- Natural Sciences and Engineering Research Council of CanadaCanadian Institutes of Health ResearchSimon Fraser UniversityMichael Smith Health Research BCCystic Fibrosis Foundation
- Mots-clés
- ProteomeProtein subcellular localization predictionArchaeaComputer scienceSubcellular localizationPrecision and recallComputational biologyInterface (matter)ProteomicsSoftwareMetagenomicsBiologyBioinformaticsData miningArtificial intelligenceBacteriaCytoplasmGeneticsGeneProgramming language
- Résumé présent dans OpenAlex
- oui