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Euk-PLoc

swMATH ID: 22420
Software Authors: Shen, H. -B.; Yang, J.; Chou, K. -C.
Description: Euk-PLoc: an ensemble classifier for large-scale eukaryotic protein subcellular location prediction. With the avalanche of newly-found protein sequences emerging in the post genomic era, it is highly desirable to develop an automated method for fast and reliably identifying their subcellular locations because knowledge thus obtained can provide key clues for revealing their functions and understanding how they interact with each other in cellular networking. However, predicting subcellular location of eukaryotic proteins is a challenging problem, particularly when unknown query proteins do not have significant homology to proteins of known subcellular locations and when more locations need to be covered. To cope with the challenge, protein samples are formulated by hybridizing the information derived from the gene ontology database and amphiphilic pseudo amino acid composition. Based on such a representation, a novel ensemble hybridization classifier was developed by fusing many basic individual classifiers through a voting system. Each of these basic classifiers was engineered by the KNN (K-Nearest Neighbor) principle. As a demonstration, a new benchmark dataset was constructed that covers the following 18 localizations: (1) cell wall, (2) centriole, (3) chloroplast, (4) cyanelle, (5) cytoplasm, (6) cytoskeleton, (7) endoplasmic reticulum, (8) extracell, (9) Golgi apparatus, (10) hydrogenosome, (11) lysosome, (12) mitochondria, (13) nucleus, (14) peroxisome, (15) plasma membrane, (16) plastid, (17) spindle pole body, and (18) vacuole. To avoid the homology bias, none of the proteins included has > or =25
Homepage: https://www.ncbi.nlm.nih.gov/pubmed/17235453
Related Software: Euk-mPLoc; Cell-PLoc; Hum-PLoc; Hum-mPLoc; Virus-ploc; iLoc-Virus; Memtype-2L; LIBSVM; Plant-mPLoc; Nuc-ploc; Signal-CF; ProtIdent; Gpos-PLoc; iLoc-Euk; PseAAC; Signal-3L; MultiLoc; Gneg-mPLoc; MultiLoc2; BLAST
Cited in: 19 Publications

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