SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartments.
Chloroplasts are organelles found in plants and involved in several important cell processes. Similarly to other compartments in the cell, chloroplasts have an internal structure comprising several sub-compartments, where different proteins are targeted to perform their functions. Given the relation between protein function and localization, the availability of effective computational tools to predict protein sub-organelle localizations is crucial for large-scale functional studies.



In this paper we present SChloro, a novel machine-learning approach to predict protein sub-chloroplastic localization, based on targeting signal detection and membrane protein information. The proposed approach performs multi-label predictions discriminating six chloroplastic sub-compartments that include inner membrane, outer membrane, stroma, thylakoid lumen, plastoglobule and thylakoid membrane. In comparative benchmarks, the proposed method outperforms current state-of-the-art methods in both single- and multi-compartment predictions, with an overall multi-label accuracy of 74%. The results demonstrate the relevance of the approach that is eligible as a good candidate for integration into more general large-scale annotation pipelines of protein subcellular localization.



The method is available as web server at http://schloro.biocomp.unibo.it



gigi@biocomp.unibo.it.
Biocomputing Group, BiGeA - CIG, Interdepartmental Center «Luigi Galvani» for Integrated Studies of Bioinformatics, Biophysics and Biocomplexity, University of Bologna, Bologna, Italy.
Castrense
C
Savojardo
Biocomputing Group, BiGeA - CIG, Interdepartmental Center «Luigi Galvani» for Integrated Studies of Bioinformatics, Biophysics and Biocomplexity, University of Bologna, Bologna, Italy.
Pier Luigi
PL
Martelli
Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Padova, Italy.
Piero
P
Fariselli
Biocomputing Group, BiGeA - CIG, Interdepartmental Center «Luigi Galvani» for Integrated Studies of Bioinformatics, Biophysics and Biocomplexity, University of Bologna, Bologna, Italy.|Interdepartmental Center «Giorgio Prodi» for Cancer Research, University of Bologna, Bologna, Italy
Rita
R
Casadio
D002736:Chloroplasts / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods*; D000069550:Machine Learning; D008565:Membrane Proteins / Q000378:metabolism; D010940:Plant Proteins / Q000378:metabolism*; D021381:Protein Transport; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D057948:Viridiplantae / Q000378:metabolism*
D008565:Membrane Proteins; D010940:Plant Proteins