LocTree3 prediction of localization.
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±3% for eukaryotes and a six-state accuracy Q6=89±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.
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany TUM Graduate School, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), 85748 Garching, Germany goldberg@rostlab.org.
Tatyana
T
Goldberg
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany.
Maximilian
M
Hecht
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany.
Tobias
T
Hamp
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany.
Timothy
T
Karl
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany Biosof LLC, New York, NY 10001, USA.
Guy
G
Yachdav
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany.
Nadeem
N
Ahmed
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany.
Uwe
U
Altermann
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany.
Philipp
P
Angerer
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany.
Sonja
S
Ansorge
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany.
Kinga
K
Balasz
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany.
Michael
M
Bernhofer
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany.
Alexander
A
Betz
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany.
Laura
L
Cizmadija
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany.
Kieu Trinh
KT
Do
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany.
Julia
J
Gerke
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany.
Robert
R
Greil
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany.
Vadim
V
Joerdens
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany.
Maximilian
M
Hastreiter
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany.
Katharina
K
Hembach
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany.
Max
M
Herzog
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany.
Maria
M
Kalemanov
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany.
Michael
M
Kluge
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany.
Alice
A
Meier
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany.
Hassan
H
Nasir
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany.
Ulrich
U
Neumaier
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany.
Verena
V
Prade
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany.
Jonas
J
Reeb
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany.
Aleksandr
A
Sorokoumov
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany.
Ilira
I
Troshani
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany.
Susann
S
Vorberg
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany.
Sonja
S
Waldraff
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany.
Jonas
J
Zierer
Center for Biological Sequence Analysis, Department of Systems Biology, DTU, 2800 Lyngby, Denmark.
Henrik
H
Nielsen
Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany Biosof LLC, New York, NY 10001, USA Institute for Advanced Study (TUM-IAS), 85748 Garching, Germany New York Consortium on Membrane Protein Structure (NYCOMPS) & Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA Institute for Food and Plant Sciences WZW - Weihenstephan, 85350 Freising, Germany.
Burkhard
B
Rost
D019843:Archaeal Proteins / Q000032:analysis; D001185:Artificial Intelligence; D001426:Bacterial Proteins / Q000032:analysis; D020407:Internet; D011506:Proteins / Q000032:analysis*; D017386:Sequence Homology, Amino Acid; D012984:Software
D019843:Archaeal Proteins; D001426:Bacterial Proteins; D011506:Proteins