@article {bioinflmu-1275,
	title = {{LocTree3 prediction of localization.}},
	journal = {Nucleic acids research},
	volume = {42},
	year = {2014},
	month = {2014 Jul},
	pages = {W350-5},
	abstract = {The prediction of protein sub-cellular localization is an important step toward elucidating protein function. For each query protein sequence, LocTree2 applies machine learning (profile kernel SVM) to predict the native sub-cellular localization in 18 classes for eukaryotes, in six for bacteria and in three for archaea. The method outputs a score that reflects the reliability of each prediction. LocTree2 has performed on par with or better than any other state-of-the-art method. Here, we report the availability of LocTree3 as a public web server. The server includes the machine learning-based LocTree2 and improves over it through the addition of homology-based inference. Assessed on sequence-unique data, LocTree3 reached an 18-state accuracy Q18=80{\textpm}3\% for eukaryotes and a six-state accuracy Q6=89{\textpm}4\% for bacteria. The server accepts submissions ranging from single protein sequences to entire proteomes. Response time of the unloaded server is about 90 s for a 300-residue eukaryotic protein and a few hours for an entire eukaryotic proteome not considering the generation of the alignments. For over 1000 entirely sequenced organisms, the predictions are directly available as downloads. The web server is available at http://www.rostlab.org/services/loctree3.},
	keywords = {Archaeal Proteins, Artificial Intelligence, Bacterial Proteins, Internet, Proteins, Sequence Homology, Amino Acid, Software},
	doi = {10.1093/nar/gku396},
	author = {Goldberg, Tatyana and Hecht, Maximilian and Hamp, Tobias and Karl, Timothy and Yachdav, Guy and Ahmed, Nadeem and Uwe Altermann and Philipp Angerer and Ansorge, Sonja and Balasz, Kinga and Michael Bernhofer and Betz, Alexander and Cizmadija, Laura and Do, Kieu Trinh and Gerke, Julia and Greil, Robert and Joerdens, Vadim and Hastreiter, Maximilian and Hembach, Katharina and Herzog, Max and Kalemanov, Maria and Michael Kluge and Meier, Alice and Nasir, Hassan and Neumaier, Ulrich and Prade, Verena and Reeb, Jonas and Sorokoumov, Aleksandr and Troshani, Ilira and Vorberg, Susann and Waldraff, Sonja and Jonas Zierer and Nielsen, Henrik and Rost, Burkhard}
}