PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis

Bioinformatics. 2005 Mar 1;21(5):617-23. doi: 10.1093/bioinformatics/bti057. Epub 2004 Oct 22.

Abstract

Motivation: PSORTb v.1.1 is the most precise bacterial localization prediction tool available. However, the program's predictive coverage and recall are low and the method is only applicable to Gram-negative bacteria. The goals of the present work are as follows: increase PSORTb's coverage while maintaining the existing precision level, expand it to include Gram-positive bacteria and then carry out a comparative analysis of localization.

Results: An expanded database of proteins of known localization and new modules using frequent subsequence-based support vector machines was introduced into PSORTb v.2.0. The program attains a precision of 96% for Gram-positive and Gram-negative bacteria and predictive coverage comparable to other tools for whole proteome analysis. We show that the proportion of proteins at each localization is remarkably consistent across species, even in species with varying proteome size.

Availability: Web-based version: http://www.psort.org/psortb. Standalone version: Available through the website under GNU General Public License.

Contact: psort-mail@sfu.ca, brinkman@sfu.ca

Supplementary information: http://www.psort.org/psortb/supplementaryinfo.html.

Publication types

  • Comparative Study
  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Bacterial Proteins / metabolism*
  • Gene Expression Profiling / methods*
  • Gram-Negative Bacteria / metabolism*
  • Gram-Positive Bacteria / metabolism*
  • Proteome / metabolism*
  • Sequence Alignment / methods
  • Sequence Analysis, Protein / methods*
  • Software*
  • Subcellular Fractions / metabolism*

Substances

  • Bacterial Proteins
  • Proteome