title: PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  http://www.psort.org/psortb (download open source software or use the web interface).
  
  
  BACKGROUND
  psort-mail@sfu.ca
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
authors.forename: Nancy Y
authors.initials: NY
authors.lastname: Yu
authors.forename: James R
authors.initials: JR
authors.lastname: Wagner
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Laird
authors.forename: Gabor
authors.initials: G
authors.lastname: Melli
authors.forename: Sébastien
authors.initials: S
authors.lastname: Rey
authors.forename: Raymond
authors.initials: R
authors.lastname: Lo
authors.forename: Phuong
authors.initials: P
authors.lastname: Dao
authors.forename: S Cenk
authors.initials: SC
authors.lastname: Sahinalp
authors.forename: Martin
authors.initials: M
authors.lastname: Ester
authors.forename: Leonard J
authors.initials: LJ
authors.lastname: Foster
authors.forename: Fiona S L
authors.initials: FS
authors.lastname: Brinkman
mesh_terms: D001105:Archaea / Q000737:chemistry*; D019843:Archaeal Proteins / Q000032:analysis*; D001419:Bacteria / Q000737:chemistry*; D001426:Bacterial Proteins / Q000032:analysis*; D040901:Proteomics / Q000379:methods; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins
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