Display Settings:

Format

Send to:

Choose Destination
See comment in PubMed Commons below
Bioinformatics. 2005 Mar 1;21(5):617-23. Epub 2004 Oct 22.

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

Author information

  • 1Department of Molecular Biology and Biochemistry, Simon Fraser University Burnaby, BC, Canada V5A 1S6.

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.

PMID:
15501914
[PubMed - indexed for MEDLINE]
Free full text
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for HighWire
    Loading ...
    Write to the Help Desk