Paper Info
Title
PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes.
Abstract
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.
Year
DOI
Venue
2010
10.1093/bioinformatics/btq249
BIOINFORMATICS
Keywords
DocType
Volume
archaea,bacteria,cross validation,web interface,protein targeting,cell wall,proteomics
Journal
26
Issue
ISSN
Citations 
13
1367-4803
17
PageRank 
References 
Authors
0.90
15
11
Name
Order
Citations
PageRank
Nancy Y. Yu1422.78
James R. Wagner2191.33
Matthew R. Laird324313.93
Gabor Melli4645.94
Sébastien Rey5412.23
Raymond Lo633123.88
Phuong Dao722314.09
Süleyman Cenk Sahinalp851744.35
Martin Ester99391858.89
Leonard J. Foster10201.48
Fiona S. L. Brinkman1155539.60