pTARGET [corrected] a new method for predicting protein subcellular localization in eukaryotes

Bioinformatics. 2005 Nov 1;21(21):3963-9. doi: 10.1093/bioinformatics/bti650. Epub 2005 Sep 6.

Abstract

Motivation: There is a scarcity of efficient computational methods for predicting protein subcellular localization in eukaryotes. Currently available methods are inadequate for genome-scale predictions with several limitations. Here, we present a new prediction method, pTARGET that can predict proteins targeted to nine different subcellular locations in the eukaryotic animal species.

Results: The nine subcellular locations predicted by pTARGET include cytoplasm, endoplasmic reticulum, extracellular/secretory, golgi, lysosomes, mitochondria, nucleus, plasma membrane and peroxisomes. Predictions are based on the location-specific protein functional domains and the amino acid compositional differences across different subcellular locations. Overall, this method can predict 68-87% of the true positives at accuracy rates of 96-99%. Comparison of the prediction performance against PSORT showed that pTARGET prediction rates are higher by 11-60% in 6 of the 8 locations tested. Besides, the pTARGET method is robust enough for genome-scale prediction of protein subcellular localizations since, it does not rely on the presence of signal or target peptides.

Availability: A public web server based on the pTARGET method is accessible at the URL http://bioinformatics.albany.edu/~ptarget. Datasets used for developing pTARGET can be downloaded from this web server. Source code will be available on request from the corresponding author.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Amino Acid Sequence
  • Animals
  • Eukaryotic Cells / metabolism*
  • Humans
  • Molecular Sequence Data
  • Proteome / chemistry*
  • Proteome / metabolism*
  • Sequence Alignment / methods*
  • Sequence Analysis, Protein / methods*
  • Software*
  • Structure-Activity Relationship
  • Subcellular Fractions / metabolism*

Substances

  • Proteome