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Article abstract


REFERENCE

Predicting subcellular localization of proteins based on their N-terminal amino acid sequence.
Olof Emanuelsson1, Henrik Nielsen2, Søren Brunak2 and Gunnar von Heijne1.
J. Mol. Biol., 300: 1005-1016, 2000.

1Stockholm Bioinformatics Center, Department of Biochemistry, Stockholm University, S-106 91 Stockholm, Sweden
2Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark, DK-2800 Lyngby, Denmark


ABSTRACT

A neural network-based tool, TargetP, for large-scale subcellular location prediction of newly identified proteins has been developed. Using N-terminal sequence information only, it discriminates between proteins destined for the mitochondrion, the chloroplast, the secretory pathway, and "other" localizations with a success rate of 85% (plant) or 90% (non-plant) on redundancy-reduced test sets. From a TargetP analysis of the recently sequenced Arabidopsis thaliana chromosomes 2 and 4 and the Ensembl Homo sapiens protein set, we estimate that 10% of all plant proteins are mitochondrial and 14% chloroplastic, and that the abundance of secretory proteins, in both Arabidopsis and Homo, is around 10%. TargetP also predicts cleavage sites with levels of correctly predicted sites ranging from approximately 40% to 50% (chloroplastic and mitochondrial presequences) to above 70% (secretory signal peptides).

PMID: 10891285




CORRESPONDENCE

Olof Emanuelsson,