YLoc-an interpretable web server for predicting subcellular localization

被引:269
作者
Briesemeister, Sebastian [1 ]
Rahnenfuehrer, Joerg [2 ]
Kohlbacher, Oliver [1 ]
机构
[1] Univ Tubingen, Div Simulat Biol Syst, Tubingen, Germany
[2] TU Dortmund Univ, Dept Stat, Dortmund, Germany
关键词
SEQUENCE; GENE; CLASSIFICATION; PROTEINS; LOCATION;
D O I
10.1093/nar/gkq477
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
070307 [化学生物学]; 071010 [生物化学与分子生物学];
摘要
Predicting subcellular localization has become a valuable alternative to time-consuming experimental methods. Major drawbacks of many of these predictors is their lack of interpretability and the fact that they do not provide an estimate of the confidence of an individual prediction. We present YLoc, an interpretable web server for predicting subcellular localization. YLoc uses natural language to explain why a prediction was made and which biological property of the protein was mainly responsible for it. In addition, YLoc estimates the reliability of its own predictions. YLoc can, thus, assist in understanding protein localization and in location engineering of proteins. The YLoc web server is available online at www.multiloc.org/YLoc.
引用
收藏
页码:W497 / W502
页数:6
相关论文
共 29 条
[1]
[Anonymous], 1993, Proceedings of the 13th International Joint Conference on Artificial Intelligence
[2]
MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction [J].
Blum, Torsten ;
Briesemeister, Sebastian ;
Kohlbacher, Oliver .
BMC BIOINFORMATICS, 2009, 10 :274
[3]
Brady Scott, 2008, Pac Symp Biocomput, P604
[4]
Going from where to why-interpretable prediction of protein subcellular localization [J].
Briesemeister, Sebastian ;
Rahnenfuehrer, Joerg ;
Kohlbacher, Oliver .
BIOINFORMATICS, 2010, 26 (09) :1232-1238
[5]
SherLoc2: A High-Accuracy Hybrid Method for Predicting Subcellular Localization of Proteins [J].
Briesemeister, Sebastian ;
Blum, Torsten ;
Brady, Scott ;
Lam, Yin ;
Kohlbacher, Oliver ;
Shatkay, Hagit .
JOURNAL OF PROTEOME RESEARCH, 2009, 8 (11) :5363-5366
[6]
Casadio Rita, 2008, Briefings in Functional Genomics & Proteomics, V7, P63, DOI 10.1093/bfgp/eln003
[7]
Prediction and classification of protein subcellular location - Sequence-order effect and pseudo amino acid composition [J].
Chou, KC ;
Cai, YD .
JOURNAL OF CELLULAR BIOCHEMISTRY, 2003, 90 (06) :1250-1260
[8]
A new hybrid approach to predict subcellular localization of proteins by incorporating gene ontology [J].
Chou, KC ;
Cai, YD .
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 2003, 311 (03) :743-747
[9]
Using functional domain composition and support vector machines for prediction of protein subcellular location [J].
Chou, KC ;
Cai, YD .
JOURNAL OF BIOLOGICAL CHEMISTRY, 2002, 277 (48) :45765-45769
[10]
Euk-mPLoc: A fusion classifier for large-scale eukaryotic protein subcellular location prediction by incorporating multiple sites [J].
Chou, Kuo-Chen ;
Shen, Hong-Bin .
JOURNAL OF PROTEOME RESEARCH, 2007, 6 (05) :1728-1734