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Prediction and classification of protein subcellular location—sequence‐order effect and pseudo amino acid composition
Author(s) -
Chou KuoChen,
Cai YuDong
Publication year - 2003
Publication title -
journal of cellular biochemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.028
H-Index - 165
eISSN - 1097-4644
pISSN - 0730-2312
DOI - 10.1002/jcb.10719
Subject(s) - pseudo amino acid composition , golgi apparatus , subcellular localization , protein sequencing , endoplasmic reticulum , biology , lysosome , biochemistry , computational biology , cytoplasm , sequence (biology) , microbiology and biotechnology , peptide sequence , gene , enzyme
Given a protein sequence, how to identify its subcellular location? With the rapid increase in newly found protein sequences entering into databanks, the problem has become more and more important because the function of a protein is closely correlated with its localization. To practically deal with the challenge, a dataset has been established that allows the identification performed among the following 14 subcellular locations: (1) cell wall, (2) centriole, (3) chloroplast, (4) cytoplasm, (5) cytoskeleton, (6) endoplasmic reticulum, (7) extracellular, (8) Golgi apparatus, (9) lysosome, (10) mitochondria, (11) nucleus, (12) peroxisome, (13) plasma membrane, and (14) vacuole. Compared with the datasets constructed by the previous investigators, the current one represents the largest in the scope of localizations covered, and hence many proteins which were totally out of picture in the previous treatments, can now be investigated. Meanwhile, to enhance the potential and flexibility in taking into account the sequence‐order effect, the series‐mode pseudo‐amino‐acid‐composition has been introduced as a representation for a protein. High success rates are obtained by the re‐substitution test, jackknife test, and independent dataset test, respectively. It is anticipated that the current automated method can be developed to a high throughput tool for practical usage in both basic research and pharmaceutical industry. © 2003 Wiley‐Liss, Inc.