Summary.
The avalanche of newly found protein sequences in the post-genomic era has motivated and challenged us to develop an automated method that can rapidly and accurately predict the localization of an uncharacterized protein in cells because the knowledge thus obtained can greatly speed up the process in finding its biological functions. However, it is very difficult to establish such a desired predictor by acquiring the key statistical information buried in a pile of extremely complicated and highly variable sequences. In this paper, based on the concept of the pseudo amino acid composition (Chou, K. C. PROTEINS: Structure, Function, and Genetics, 2001, 43: 246–255), the approach of cellular automata image is introduced to cope with this problem. Many important features, which are originally hidden in the long amino acid sequences, can be clearly displayed through their cellular automata images. One of the remarkable merits by doing so is that many image recognition tools can be straightforwardly applied to the target aimed here. High success rates were observed through the self-consistency, jackknife, and independent dataset tests, respectively.
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MV Boland MK Markey RF Murphy (1998) ArticleTitleAutomated recognition of patterns characteristic of subcellular structures in fluorescence microscopy images. Cytometry 33 366–375 Occurrence Handle10.1002/(SICI)1097-0320(19981101)33:3<366::AID-CYTO12>3.0.CO;2-R Occurrence Handle1:STN:280:DyaK1M%2FjvVWnsQ%3D%3D Occurrence Handle9822349
YD Cai (2001) ArticleTitleIs it a paradox or misinterpretation. PROTEINS: Structure, Function, and Genetics 43 336–338 Occurrence Handle10.1002/prot.1045 Occurrence Handle1:CAS:528:DC%2BD3MXjtFOlsL4%3D
YD Cai KC Chou (2003) ArticleTitleNearest neighbour algorithm for predicting protein subcellular location by combining functional domain composition and pseudo-amino acid composition. Biochem Biophys Res Comm 305 407–411 Occurrence Handle1:CAS:528:DC%2BD3sXjs1erurg%3D Occurrence Handle12745090
YD Cai KC Chou (2004a) ArticleTitlePredicting 22 protein localizations in budding yeast. Biochem Biophys Res Comm 323 425–428 Occurrence Handle10.1016/j.bbrc.2004.08.113 Occurrence Handle1:CAS:528:DC%2BD2cXnsVyqtr4%3D
YD Cai KC Chou (2004b) ArticleTitlePredicting subcellular localization of proteins in a hybridization space. Bioinformatics 20 1151–1156 Occurrence Handle1:CAS:528:DC%2BD2cXjs1Wrt78%3D
YD Cai XJ Liu XB Xu KC Chou (2002a) ArticleTitleSupport vector machines for prediction of protein subcellular location by incorporating quasi-sequence-order effect. J Cell Biochem 84 343–348 Occurrence Handle10.1002/jcb.10030
YD Cai XJ Liu XB Xu KC Chou (2002b) ArticleTitleSVM for predicting membrane protein types by incorporating quasi-sequence-order effect. Internet. Electronic Journal of Molecular Design 1 219–226 Occurrence Handle1:CAS:528:DC%2BD38XlvVCit7s%3D
YD Cai GP Zhou KC Chou (2003) ArticleTitleSupport vector machines for predicting membrane protein types by using functional domain composition. Biophys J 84 3257–3263 Occurrence Handle1:CAS:528:DC%2BD3sXjvFGju7o%3D Occurrence Handle12719255
YD Cai GP Zhou KC Chou (2005) ArticleTitlePredicting enzyme family classes by hybridizing gene product composition and pseudo-amino acid composition. J Theor Biol 234 145–149 Occurrence Handle10.1016/j.jtbi.2004.11.017 Occurrence Handle1:CAS:528:DC%2BD2MXhtlOkt74%3D Occurrence Handle15721043
J Cedano P Aloy JA P’erez-Pons E Querol (1997) ArticleTitleRelation between amino acid composition and cellular location of proteins. J Mol Biol 266 594–600 Occurrence Handle10.1006/jmbi.1996.0804 Occurrence Handle1:CAS:528:DyaK2sXhslKksL4%3D Occurrence Handle9067612
KC Chou (1995) ArticleTitleA novel approach to predicting protein structural classes in a (20–1)-D amino acid composition space. Proteins: Structure, Function & Genetics 21 319–344 Occurrence Handle1:CAS:528:DyaK2MXls12rsb0%3D
KC Chou (2000a) ArticleTitlePrediction of protein subcellular locations by incorporating quasi-sequence-order effect. Biochem Biophys Res Commun 278 477–483 Occurrence Handle10.1006/bbrc.2000.3815 Occurrence Handle1:CAS:528:DC%2BD3cXotlKksbs%3D
KC Chou (2000b) ArticleTitleReview: Prediction of protein structural classes and subcellular locations. Curr Protein Pept Sci 1 171–208 Occurrence Handle10.2174/1389203003381379 Occurrence Handle1:CAS:528:DC%2BD3cXnsVeisL0%3D
KC Chou (2001) ArticleTitlePrediction of protein cellular attributes using pseudo-amino-acid-composition. PROTEINS: Structure, Function, and Genetics 43 246–255 Occurrence Handle10.1002/prot.1035 Occurrence Handle1:CAS:528:DC%2BD3MXjtFOls74%3D
Chou KC (2002) A new branch of proteomics: prediction of protein cellular attributes. In: Weinrer PW, Lu Q (eds) Gene cloning & expression technologies, Chapter 4. Eaton Publishing, Westborough, MA, pp 57–70
KC Chou (2005) ArticleTitleUsing amphiphilic pseudo amino acid composition to predict enzyme subfamily classes. Bioinformatics 21 10–19 Occurrence Handle10.1093/bioinformatics/bth466 Occurrence Handle1:CAS:528:DC%2BD2MXisVWitw%3D%3D Occurrence Handle15308540
KC Chou YD Cai (2002) ArticleTitleUsing functional domain composition and support vector machines for prediction of protein subcellular location. J Biol Chem 277 45765–45769 Occurrence Handle1:CAS:528:DC%2BD38XovFKjurg%3D Occurrence Handle12186861
KC Chou YD Cai (2003a) ArticleTitlePredicting protein quaternary structure by pseudo amino acid composition. PROTEINS: Structure, Function, and Genetics 53 282–289 Occurrence Handle10.1002/prot.10500 Occurrence Handle1:CAS:528:DC%2BD3sXotVSqurk%3D
KC Chou YD Cai (2003b) ArticleTitlePrediction and classification of protein subcellular location: sequence-order effect and pseudo amino acid composition. J Cell Biochem 90 1250–1260 Occurrence Handle10.1002/jcb.10719 Occurrence Handle1:CAS:528:DC%2BD3sXpslSgsb4%3D
KC Chou YD Cai (2004a) ArticleTitlePredicting protein structural class by functional domain composition. Biochem Biophys Res Comm 321 1007–1009 Occurrence Handle10.1016/j.bbrc.2004.07.059 Occurrence Handle1:CAS:528:DC%2BD2cXmt1Ogtb0%3D
KC Chou YD Cai (2004b) ArticleTitlePredicting subcellular localization of proteins by hybridizing functional domain composition and pseudo-amino acid composition. J Cell Biochem 91 1197–1203 Occurrence Handle10.1002/jcb.10790 Occurrence Handle1:CAS:528:DC%2BD2cXjt1yntrY%3D
KC Chou YD Cai (2004c) ArticleTitlePrediction of protein subcellular locations by GO-FunD-PseAA predicor. Biochem Biophys Res Commun 320 1236–1239 Occurrence Handle10.1016/j.bbrc.2004.06.073 Occurrence Handle1:CAS:528:DC%2BD2cXls1eisL0%3D
KC Chou YD Cai (2005) ArticleTitlePredicting protein localization in budding yeast. Bioinformatics 21 944–950 Occurrence Handle10.1093/bioinformatics/bth466 Occurrence Handle1:CAS:528:DC%2BD2MXis1Oquro%3D Occurrence Handle15513989
KC Chou DW Elrod (1999) ArticleTitleProtein subcellular location prediction. Protein Engineering 12 107–118 Occurrence Handle10.1093/protein/12.2.107 Occurrence Handle1:CAS:528:DyaK1MXhvFehs7g%3D Occurrence Handle10195282
JJ Chou CT Zhang (1993) ArticleTitleA joint prediction of the folding types of 1490 human proteins from their genetic codons. J Theor Biol 161 251–262 Occurrence Handle10.1006/jtbi.1993.1053 Occurrence Handle1:CAS:528:DyaK3sXkvV2ns7g%3D Occurrence Handle8331952
KC Chou CT Zhang (1994) ArticleTitlePredicting protein folding types by distance functions that make allowances for amino acid interactions. J Biol Chem 269 22014–22020 Occurrence Handle1:CAS:528:DyaK2cXlslCls7o%3D Occurrence Handle8071322
KC Chou CT Zhang (1995) ArticleTitleReview: Prediction of protein structural classes. Crit Rev Biochem Mol Biol 30 275–349 Occurrence Handle1:CAS:528:DyaK2MXosFentb8%3D Occurrence Handle7587280
KC Chou W Liu GM Maggiora CT Zhang (1998) ArticleTitlePrediction and classification of domain structural classes. PROTEINS: Structure, Function, and Genetics 31 97–103 Occurrence Handle10.1002/(SICI)1097-0134(19980401)31:1<97::AID-PROT8>3.0.CO;2-E Occurrence Handle1:CAS:528:DyaK1cXit1yms70%3D
Y Gao SH Shao X Xiao YS Ding YS Huang ZD Huang KC Chou (2005) ArticleTitleUsing pseudo amino acid composition to predict protein subcellular location: approached with Lyapunov index, Bessel function, and Chebyshev filter. Amino Acids 28 373–376 Occurrence Handle10.1007/s00726-005-0206-9 Occurrence Handle1:CAS:528:DC%2BD2MXlt1Kmurw%3D Occurrence Handle15889221
VD Gusev LA Nemytikova NA Chuzhanova (2001) ArticleTitleA rapid method for detecting interconnections between functionally and/or evolutionary close biological sequences. Mol Biol (Mosk) 35 1015–1022 Occurrence Handle1:STN:280:DC%2BD38%2Fkt1Knsg%3D%3D
J Haddadnia K Faez M Ahmadi (2002) ArticleTitleA neural based human face recognition system using an efficient feature extraction method with pseudo zernike moment. J Circuits, Systems, and Computers 11 283–304
RF Murphy MV Boland M Velliste (2000) ArticleTitleTowards a systematics for protein subcellular location: quantitative description of protein localization patterns and automated analysis of fluorescence microscope images. Proc Int Conf Intell Syst Mol Biol 8 251–259 Occurrence Handle1:STN:280:DC%2BD3M7gt1aksQ%3D%3D Occurrence Handle10977086
K Nakai (2000) ArticleTitleProtein sorting signals and prediction of subcellular localization. Adv Protein Chem 54 277–344 Occurrence Handle10.1016/S0065-3233(00)54009-1 Occurrence Handle1:CAS:528:DC%2BD3cXltFSqs70%3D Occurrence Handle10829231
YX Pan ZZ Zhang ZM Guo GY Feng ZD Huang L He (2003) ArticleTitleApplication of pseudo amino acid composition for predicting protein subcellular location: stochastic signal processing approach. J Protein Chem 22 395–402 Occurrence Handle10.1023/A:1025350409648 Occurrence Handle1:CAS:528:DC%2BD3sXmsFejs7s%3D Occurrence Handle13678304
KJ Park M Kanehisa (2003) ArticleTitlePrediction of protein subcellular locations by support vector machines using compositions of amino acid and amino acid pairs. Bioinformatics 19 1656–1663 Occurrence Handle1:CAS:528:DC%2BD3sXnt1Gqu78%3D Occurrence Handle12967962
J Portilla EP Simoncelli (2000) ArticleTitleA parametric texture model based on joint statistics of complex wavelet coefficients. Int J Comput Vision 40 49–71 Occurrence Handle10.1023/A:1026553619983
M Wang J Yang GP Liu ZJ Xu KC Chou (2004a) ArticleTitleWeighted-support vector machines for predicting membrane protein types based on pseudo amino acid composition. Protein Eng Des Sel 17 509–516 Occurrence Handle1:CAS:528:DC%2BD2cXos1GisLY%3D
M Wang J Yang ZJ Xu KC Chou (2004b) ArticleTitleSLLE for predicting membrane protein types. J Theor Biol 232 7–15
M Wang JS Yao ZD Huang ZJ Xu GP Liu HY Zhao XY Wang J Yang YS Zhu KC Chou (2005) ArticleTitleA new nucleotide-composition based fingerprint of SARS-CoV with visualization analysis. Med Chem 1 39–47 Occurrence Handle1:CAS:528:DC%2BD2MXhsVWktbk%3D
Wolfram S (2002) A new kind of science. Wolfram Media Inc., Champaign, IL
X Xiao S Shao Y Dingl Z Huang Y Huang KC Chou (2005a) ArticleTitleUsing complexity measure factor to predict protein subcellular location. Amino Acids 28 57–61 Occurrence Handle1:CAS:528:DC%2BD2MXhsVKqsro%3D
X Xiao S Shao Y Ding Z Huang X Chen KC Chou (2005b) ArticleTitleAn application of gene comparative image for predicting the effect on replication ratio by HBV virus gene missense mutation. J Theor Biol 235 555–565 Occurrence Handle10.1016/j.jtbi.2005.02.008 Occurrence Handle1:CAS:528:DC%2BD2MXltVelt7c%3D
X Xiao S Shao Y Ding Z Huang X Chen KC Chou (2005c) ArticleTitleUsing cellular automata to generate Image representation for biological sequences. Amino Acids 28 29–35 Occurrence Handle1:CAS:528:DC%2BD2MXhsVKqs70%3D
GP Zhou (1998) ArticleTitleAn intriguing controversy over protein structural class prediction. J Protein Chem 17 729–738 Occurrence Handle10.1023/A:1020713915365 Occurrence Handle1:CAS:528:DyaK1MXnslaltw%3D%3D Occurrence Handle9988519
GP Zhou N Assa-Munt (2001) ArticleTitleSome insights into protein structural class prediction. PROTEINS: Structure, Function, and Genetics 44 57–59 Occurrence Handle1:CAS:528:DC%2BD3MXktlSnsbk%3D
GP Zhou K Doctor (2003) ArticleTitleSubcellular location prediction of apoptosis proteins. PROTEINS: Structure, Function, and Genetics 50 44–48 Occurrence Handle10.1002/prot.10251 Occurrence Handle1:CAS:528:DC%2BD3sXlsVKmug%3D%3D
SC Zhu Y Wu D Mumford (1997) ArticleTitleMinimax entropy principle and its application to texture modeling. Neural comput 9 1627–1660
J Ziv A Lempel (1976) ArticleTitleOn the complexity of finite sequences. IEEE Trans Inf Theor IT-22 75–81
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Xiao, X., Shao, S., Ding, Y. et al. Using cellular automata images and pseudo amino acid composition to predict protein subcellular location. Amino Acids 30, 49–54 (2006). https://doi.org/10.1007/s00726-005-0225-6
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DOI: https://doi.org/10.1007/s00726-005-0225-6