|
TargetP
|
extracellular, mitochondrial, chloroplast |
non-plant, plant |
Emanuelsson, O., Nielsen, H., Brunak, S., & von Heijne, G.
(2000)
Predicting subcellular localization of proteins based on their N-terminal amino acid sequence.
Journal of molecular biology,
300(4), 1005-1016.
|
|
TMHMM
|
transmembrane helices |
any |
Krogh, A., Larsson, B., von Heijne, G., & Sonnhammer, E. L.
(2001)
Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.
Journal of molecular biology,
305(3), 567-580.
|
|
scanProsite (PS-Scan)
|
ER retention signal |
any |
de Castro E, Sigrist CJ, Gattiker A, Bulliard V, Langendijk-Genevaux PS, Gasteiger E, Bairoch A, Hulo N.
(2006)
ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins.
Nucleic Acids Res.,
34(Web Server issue), W362-365.
|
|
SecretomeP 2.0
|
non-classical i.e. not signal peptide triggered protein secretion |
gram-positive bacteria, gram-negative bacteria, mammal |
Bendtsen J.D., Jensen,L.J., Blom,N., et al.
(2004)
Feature based prediction of non-classical and leaderless protein secretion.
Protein Eng. Des. Sel.,
17, 349-356.
|
|
Phobius
|
signal peptide and transmembrane topology |
any |
Käll, L., Krogh, A., & Sonnhammer, E. L. L.
(2007)
Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server..
Nucleic Acids Res.,
35(Web Server issue), W429-432.
|
|
WoLF PSORT
|
> 5 locations |
fungi, plant, animal |
Horton, P., Park, K.-J., Obayashi, T., Fujita, N., Harada, H., Adams-Collier, C. J., & Nakai, K.
(2007)
WoLF PSORT: protein localization predictor.
Nucleic Acids Res.,
35(Web Server issue), W585-587.
|
|
PRED-LIPO
|
lipoprotein signal peptides |
gram-positive bacteria |
Bagos, Pantelis G, Tsirigos, K. D., Liakopoulos, T. D., & Hamodrakas, S. J.
(2008)
Prediction of lipoprotein signal peptides in Gram-positive bacteria with a Hidden Markov Model.
Journal of proteome research,
7(12), 5082-5093.
|
|
ProLoc-GO
|
> 5 locations |
human and eukaryotes |
Huang, W.-L., Tung, C.-W., Ho, S.-W., Hwang, S.-F., & Ho, S.-Y.
(2008)
ProLoc-GO: utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization.
BMC bioinformatics,
9, 80.
|
|
KnowPredsite
|
> 5 locations |
prokaryotes and eukaryotes |
Lin, H.-N., Chen, C.-T., Sung, T.-Y., Ho, S.-Y., & Hsu, W.-L.
(2009)
Protein subcellular localization prediction of eukaryotes using a knowledge-based approach.
BMC bioinformatics,
10 Suppl 15, S8.
|
|
MultiLoc2
|
> 5 locations |
animal, fungal, plant |
Blum, T, Briesemeister, S, and Kohlbacher, O
(2009)
MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction.
BMC Bioinformatics,
10:274.
|
|
PRED-SIGNAL
|
signal peptides |
archaea |
Bagos, P G, Tsirigos, K. D., Plessas, S. K., Liakopoulos, T. D., & Hamodrakas, S. J.
(2009)
Prediction of signal peptides in archaea.
Protein engineering, design & selection: PEDS,
22(1), 27-35.
|
|
RSLPred
|
chloroplast, cytoplasm, mitochondria, nucleus |
oryza sativa only |
Kaundal, R., & Raghava, G. P. S.
(2009)
RSLpred: an integrative system for predicting subcellular localization of rice proteins combining compositional and evolutionary information.
Proteomics,
9(9), 2324-2342.
|
|
SherLoc2
|
> 5 locations |
animal, fungi, plant |
Briesemeister, S., Blum, T., Brady, S., Lam, Y., Kohlbacher, O., & Shatkay, H.
(2009)
SherLoc2: a high-accuracy hybrid method for predicting subcellular localization of proteins.
Journal of proteome research,
8(11), 5363-5366.
|
|
Cell-PLoc 2.0
|
> 5 locations |
eukaryote, human, plant, virus, gram-positive bacteria, gram-negative bacteria |
Chou, K. and Shen, H.
(2010)
Cell-PLoc 2.0: an improved package of web-servers for predicting subcellular localization of proteins in various organisms.
Natural Science,
2, 1090-1103.
|
|
CoBaltDB
|
> 5 locations |
prokaryotes |
Goudenège, D., Avner, S., Lucchetti-Miganeh, C., & Barloy-Hubler, F.
(2010)
CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources.
BMC microbiology,
10, 88.
|
|
PSORTb
|
> 5 locations |
gram-positive and gram-negative bacteria |
Yu, N. Y., Wagner, J. R., Laird, M. R., Melli, G., Rey, S., Lo, R., ... Brinkman, F. S. L.
(2010)
PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes.
Bioinformatics (Oxford, England),
26(13), 1608-1615.
|
|
SCLPred
|
cytoplasm, mitochondrion, nucleus, secretory, chloroplast |
animals, plants, fungi |
Mooney, C., Wang, Y.-H., & Pollastri, G.
(2011)
SCLpred: protein subcellular localization prediction by N-to-1 neural networks.
Bioinformatics (Oxford, England),
27(20), 2812-2819.
|
|
SignalP 4.0
|
signal peptide |
eukaryotic, gram-positive bacteria, gram-negative bacteria |
Petersen, T. N., Brunak, S., von Heijne, G., & Nielsen, H.
(2011)
SignalP 4.0: discriminating signal peptides from transmembrane regions.
Nature methods,
8(10), 785-786.
|
|
SlocX
|
> 5 locations |
aribdopsis thaliana only |
Ryngajllo, M., Childs, L., Lohse, M., Giorgi, F. M., Lude, A., Selbig, J., & Usadel, B.
(2011)
SLocX: Predicting Subcellular Localization of Arabidopsis Proteins Leveraging Gene Expression Data.
Frontiers in plant science,
2, 43.
|
|
APSLAP
|
> 5 locations |
apoptosis |
Saravanan, V., & Lakshmi, P. T. V.
(2013)
APSLAP: An Adaptive Boosting Technique for Predicting Subcellular Localization of Apoptosis Protein.
Acta biotheoretica,
.
|
|
Iloc Animal
|
> 5 locations |
animal |
Lin, W.-Z., Fang, J.-A., Xiao, X., & Chou, K.-C.
(2013)
iLoc-Animal: a multi-label learning classifier for predicting subcellular localization of animal proteins.
Molecular bioSystems,
9(4), 634-644.
|