SherLoc2: a high-accuracy hybrid method for predicting subcellular localization of proteins

J Proteome Res. 2009 Nov;8(11):5363-6. doi: 10.1021/pr900665y.

Abstract

SherLoc2 is a comprehensive high-accuracy subcellular localization prediction system. It is applicable to animal, fungal, and plant proteins and covers all main eukaryotic subcellular locations. SherLoc2 integrates several sequence-based features as well as text-based features. In addition, we incorporate phylogenetic profiles and Gene Ontology (GO) terms derived from the protein sequence to considerably improve the prediction performance. SherLoc2 achieves an overall classification accuracy of up to 93% in 5-fold cross-validation. A novel feature, DiaLoc, allows users to manually provide their current background knowledge by describing a protein in a short abstract which is then used to improve the prediction. SherLoc2 is available both as a free Web service and as a stand-alone version at http://www-bs.informatik.uni-tuebingen.de/Services/SherLoc2.

Publication types

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

MeSH terms

  • Animals
  • Fungal Proteins* / analysis
  • Fungal Proteins* / classification
  • Phylogeny
  • Plant Proteins* / analysis
  • Plant Proteins* / classification
  • Proteins* / analysis
  • Proteins* / classification
  • Reproducibility of Results
  • Software*
  • Subcellular Fractions / chemistry*

Substances

  • Fungal Proteins
  • Plant Proteins
  • Proteins