title: TPpred3 detects and discriminates mitochondrial and chloroplastic targeting peptides in eukaryotic proteins.
abstract: BACKGROUND
  Molecular recognition of N-terminal targeting peptides is the most common mechanism controlling the import of nuclear-encoded proteins into mitochondria and chloroplasts. When experimental information is lacking, computational methods can annotate targeting peptides, and determine their cleavage sites for characterizing protein localization, function, and mature protein sequences. The problem of discriminating mitochondrial from chloroplastic propeptides is particularly relevant when annotating proteomes of photosynthetic Eukaryotes, endowed with both types of sequences.
  
  
  RESULTS
  Here, we introduce TPpred3, a computational method that given any Eukaryotic protein sequence performs three different tasks: (i) the detection of targeting peptides; (ii) their classification as mitochondrial or chloroplastic and (iii) the precise localization of the cleavage sites in an organelle-specific framework. Our implementation is based on our TPpred previously introduced. Here, we integrate a new N-to-1 Extreme Learning Machine specifically designed for the classification task (ii). For the last task, we introduce an organelle-specific Support Vector Machine that exploits sequence motifs retrieved with an extensive motif-discovery analysis of a large set of mitochondrial and chloroplastic proteins. We show that TPpred3 outperforms the state-of-the-art methods in all the three tasks.
  
  
  METHODS
  The method server and datasets are available at http://tppred3.biocomp.unibo.it.
  
  
  BACKGROUND
  gigi@biocomp.unibo.it
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Biocomputing Group, University of Bologna, Department of Biology, 40126 Bologna, Italy and.
authors.forename: Castrense
authors.initials: C
authors.lastname: Savojardo
authors.affiliation: Biocomputing Group, University of Bologna, Department of Biology, 40126 Bologna, Italy and.
authors.forename: Pier Luigi
authors.initials: PL
authors.lastname: Martelli
authors.affiliation: Biocomputing Group, University of Bologna, Department of Biology, 40126 Bologna, Italy and Department of Computer Science and Engineering, University of Bologna, 40127 Bologna, Italy.
authors.forename: Piero
authors.initials: P
authors.lastname: Fariselli
authors.affiliation: Biocomputing Group, University of Bologna, Department of Biology, 40126 Bologna, Italy and.
authors.forename: Rita
authors.initials: R
authors.lastname: Casadio
mesh_terms: D060365:Chloroplast Proteins / Q000737:chemistry* / Q000378:metabolism; D002736:Chloroplasts / Q000378:metabolism; D056890:Eukaryota / Q000378:metabolism; D000069550:Machine Learning; D008928:Mitochondria / Q000378:metabolism; D024101:Mitochondrial Proteins / Q000737:chemistry* / Q000378:metabolism; D010455:Peptides / Q000737:chemistry; D021381:Protein Transport; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D060388:Support Vector Machine
chemical_list: D060365:Chloroplast Proteins; D024101:Mitochondrial Proteins; D010455:Peptides