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PROlocalizer: integrated web service for protein subcellular localization prediction.

Laurila K, Vihinen M - Amino Acids (2010)

Bottom Line: Subcellular localization is an important protein property, which is related to function, interactions and other features.As experimental determination of the localization can be tedious, especially for large numbers of proteins, a number of prediction tools have been developed.We developed the PROlocalizer service that integrates 11 individual methods to predict altogether 12 localizations for animal proteins.

View Article: PubMed Central - PubMed

Affiliation: Department of Signal Processing, Tampere University of Technology, Tampere, Finland.

ABSTRACT
Subcellular localization is an important protein property, which is related to function, interactions and other features. As experimental determination of the localization can be tedious, especially for large numbers of proteins, a number of prediction tools have been developed. We developed the PROlocalizer service that integrates 11 individual methods to predict altogether 12 localizations for animal proteins. The method allows the submission of a number of proteins and mutations and generates a detailed informative document of the prediction and obtained results. PROlocalizer is available at http://bioinf.uta.fi/PROlocalizer/ .

Show MeSH
PROlocalizer prediction scheme. The service predicts proteins to 12 compartments: C cytosol; ER endoplasmic reticulum, lumen; Gtm Golgi, transmembrane; Mtm mitochondrial inner membrane (transmembrane); Mps mitochondrial periplasmic space; Mma mitochondrial matrix; PM plasma membrane; S secreted; N nucleus; P peroxisome; gPM plasma membrane, GPI anchor; and mPM plasma membrane, myristoylated. Programs run locally are indicated with black box. In some rare cases double localizations are predicted if the reliability coefficient (RC) in TargetP is high, i.e. poor
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Fig1: PROlocalizer prediction scheme. The service predicts proteins to 12 compartments: C cytosol; ER endoplasmic reticulum, lumen; Gtm Golgi, transmembrane; Mtm mitochondrial inner membrane (transmembrane); Mps mitochondrial periplasmic space; Mma mitochondrial matrix; PM plasma membrane; S secreted; N nucleus; P peroxisome; gPM plasma membrane, GPI anchor; and mPM plasma membrane, myristoylated. Programs run locally are indicated with black box. In some rare cases double localizations are predicted if the reliability coefficient (RC) in TargetP is high, i.e. poor

Mentions: PROlocalizer service implements the Scandinavian protocol of Emanuelsson et al. The method can be applied to animal proteins as the signals and localization machinery are well conserved in metazoans. The protocol can predict altogether 12 individual subcellular localizations, which are mitochondrial inner membrane, transmembrane; mitochondrial periplasmic space; mitochondrial matrix; Golgi, transmembrane; plasma membrane; secreted; ER lumen; nucleus; peroxisome; cytoplasmic; plasma membrane, GPI anchor; and plasma membrane, myristoylated. The prediction scheme is in Fig. 1. PROlocalizer is freely accessible for academic use at http://bioinf.uta.fi/PROlocalizer.Fig. 1


PROlocalizer: integrated web service for protein subcellular localization prediction.

Laurila K, Vihinen M - Amino Acids (2010)

PROlocalizer prediction scheme. The service predicts proteins to 12 compartments: C cytosol; ER endoplasmic reticulum, lumen; Gtm Golgi, transmembrane; Mtm mitochondrial inner membrane (transmembrane); Mps mitochondrial periplasmic space; Mma mitochondrial matrix; PM plasma membrane; S secreted; N nucleus; P peroxisome; gPM plasma membrane, GPI anchor; and mPM plasma membrane, myristoylated. Programs run locally are indicated with black box. In some rare cases double localizations are predicted if the reliability coefficient (RC) in TargetP is high, i.e. poor
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3040813&req=5

Fig1: PROlocalizer prediction scheme. The service predicts proteins to 12 compartments: C cytosol; ER endoplasmic reticulum, lumen; Gtm Golgi, transmembrane; Mtm mitochondrial inner membrane (transmembrane); Mps mitochondrial periplasmic space; Mma mitochondrial matrix; PM plasma membrane; S secreted; N nucleus; P peroxisome; gPM plasma membrane, GPI anchor; and mPM plasma membrane, myristoylated. Programs run locally are indicated with black box. In some rare cases double localizations are predicted if the reliability coefficient (RC) in TargetP is high, i.e. poor
Mentions: PROlocalizer service implements the Scandinavian protocol of Emanuelsson et al. The method can be applied to animal proteins as the signals and localization machinery are well conserved in metazoans. The protocol can predict altogether 12 individual subcellular localizations, which are mitochondrial inner membrane, transmembrane; mitochondrial periplasmic space; mitochondrial matrix; Golgi, transmembrane; plasma membrane; secreted; ER lumen; nucleus; peroxisome; cytoplasmic; plasma membrane, GPI anchor; and plasma membrane, myristoylated. The prediction scheme is in Fig. 1. PROlocalizer is freely accessible for academic use at http://bioinf.uta.fi/PROlocalizer.Fig. 1

Bottom Line: Subcellular localization is an important protein property, which is related to function, interactions and other features.As experimental determination of the localization can be tedious, especially for large numbers of proteins, a number of prediction tools have been developed.We developed the PROlocalizer service that integrates 11 individual methods to predict altogether 12 localizations for animal proteins.

View Article: PubMed Central - PubMed

Affiliation: Department of Signal Processing, Tampere University of Technology, Tampere, Finland.

ABSTRACT
Subcellular localization is an important protein property, which is related to function, interactions and other features. As experimental determination of the localization can be tedious, especially for large numbers of proteins, a number of prediction tools have been developed. We developed the PROlocalizer service that integrates 11 individual methods to predict altogether 12 localizations for animal proteins. The method allows the submission of a number of proteins and mutations and generates a detailed informative document of the prediction and obtained results. PROlocalizer is available at http://bioinf.uta.fi/PROlocalizer/ .

Show MeSH