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Volumn 1824, Issue 12, 2012, Pages 1425-1433

MetaLocGramN: A meta-predictor of protein subcellular localization for Gram-negative bacteria

Author keywords

Artificial Neural Network; Gram negative bacteria; Linear regression; Machine learning; Meta server; Subcellular localization

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ANALYTIC METHOD; BACTERIAL CELL; CELL COMPARTMENTALIZATION; CELL MEMBRANE; CELLULAR DISTRIBUTION; CONFERENCE PAPER; CYTOPLASM; EXTRACELLULAR SPACE; GRAM NEGATIVE BACTERIUM; LOGISTIC REGRESSION ANALYSIS; MATHEMATICAL COMPUTING; NONHUMAN; OUTER MEMBRANE; PRIORITY JOURNAL; PROTEIN LOCALIZATION;

EID: 84867678748     PISSN: 15709639     EISSN: 18781454     Source Type: Journal    
DOI: 10.1016/j.bbapap.2012.05.018     Document Type: Conference Paper
Times cited : (26)

References (51)
  • 1
    • 1042264072 scopus 로고    scopus 로고
    • Protein localization in proteomics
    • DOI 10.1016/j.cbpa.2003.11.003
    • T.N. Davis Protein localization in proteomics Curr. Opin. Chem. Biol. 8 2004 49 53 (Pubitemid 38201477)
    • (2004) Current Opinion in Chemical Biology , vol.8 , Issue.1 , pp. 49-53
    • Davis, T.N.1
  • 2
    • 0031588694 scopus 로고    scopus 로고
    • Relation between amino acid composition and cellular location of proteins
    • DOI 10.1006/jmbi.1996.0804
    • J. Cedano, P. Aloy, J.A. Perez-Pons, and E. Querol Relation between amino acid composition and cellular location of proteins J. Mol. Biol. 266 1997 594 600 (Pubitemid 27117290)
    • (1997) Journal of Molecular Biology , vol.266 , Issue.3 , pp. 594-600
    • Cedano, J.1    Aloy, P.2    Perez-Pons, J.A.3    Querol, E.4
  • 3
    • 8844261813 scopus 로고    scopus 로고
    • Translocation of bacterial proteins - An overview
    • DOI 10.1016/j.bbamcr.2004.02.007, PII S0167488904000783
    • I.B. Holland Translocation of bacterial proteins - an overview Biochim. Biophys. Acta, Mol. Cell. Res. 1694 2004 5 16 (Pubitemid 39535058)
    • (2004) Biochimica et Biophysica Acta - Molecular Cell Research , vol.1694 , Issue.1-3 SPEC.ISS. , pp. 5-16
    • Holland, I.B.1
  • 4
    • 0034891203 scopus 로고    scopus 로고
    • Translocation of proteins across the cell envelope of Gram-positive bacteria
    • DOI 10.1016/S0168-6445(01)00062-6, PII S0168644501000626
    • K.H. van Wely, J. Swaving, R. Freudl, and A.J. Driessen Translocation of proteins across the cell envelope of Gram-positive bacteria FEMS Microbiol. Rev. 25 2001 437 454 (Pubitemid 32778468)
    • (2001) FEMS Microbiology Reviews , vol.25 , Issue.4 , pp. 437-454
    • Van Wely, K.H.M.1    Swaving, J.2    Freudl, R.3    Driessen, A.J.M.4
  • 5
    • 33748878164 scopus 로고    scopus 로고
    • Methods for predicting bacterial protein subcellular localization
    • DOI 10.1038/nrmicro1494, PII NRMICRO1494
    • J.L. Gardy, and F.S. Brinkman Methods for predicting bacterial protein subcellular localization Nat. Rev. Microbiol. 4 2006 741 751 (Pubitemid 44420125)
    • (2006) Nature Reviews Microbiology , vol.4 , Issue.10 , pp. 741-751
    • Gardy, J.L.1    Brinkman, F.S.L.2
  • 6
    • 77952811130 scopus 로고    scopus 로고
    • Going from where to why - Interpretable prediction of protein subcellular localization
    • S. Briesemeister, J. Rahnenfuhrer, and O. Kohlbacher Going from where to why - interpretable prediction of protein subcellular localization Bioinformatics 26 2010 1232 1238
    • (2010) Bioinformatics , vol.26 , pp. 1232-1238
    • Briesemeister, S.1    Rahnenfuhrer, J.2    Kohlbacher, O.3
  • 7
    • 78449279166 scopus 로고    scopus 로고
    • Prediction of subcellular locations of proteins: Where to proceed?
    • K. Imai, and K. Nakai Prediction of subcellular locations of proteins: where to proceed? Proteomics 10 2010 3970 3983
    • (2010) Proteomics , vol.10 , pp. 3970-3983
    • Imai, K.1    Nakai, K.2
  • 8
    • 36549082406 scopus 로고    scopus 로고
    • Computational prediction of subcellular localization
    • DOI 10.1385/1-59745-466-4:429, Protein Targeting Protocols, Second Edition
    • K. Nakai, and P. Horton Computational prediction of subcellular localization Methods Mol. Biol. 390 2007 429 466 (Pubitemid 350183676)
    • (2007) Methods in Molecular Biology , vol.390 , pp. 429-466
    • Nakai, K.1    Horton, P.2
  • 9
    • 77954199597 scopus 로고    scopus 로고
    • PSORTb 3.0: Improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes
    • N.Y. Yu, J.R. Wagner, M.R. Laird, G. Melli, S. Rey, R. Lo, P. Dao, S.C. Sahinalp, M. Ester, L.J. Foster, and F.S. Brinkman PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes Bioinformatics 26 2010 1608 1615
    • (2010) Bioinformatics , vol.26 , pp. 1608-1615
    • Yu, N.Y.1    Wagner, J.R.2    Laird, M.R.3    Melli, G.4    Rey, S.5    Lo, R.6    Dao, P.7    Sahinalp, S.C.8    Ester, M.9    Foster, L.J.10    Brinkman, F.S.11
  • 10
    • 84867690831 scopus 로고    scopus 로고
    • The development of a metaserver for prediction of protein subcellular localization in bacterial cells and its application to identification of periplasmic proteins in selected Epsilon-proteobacteria
    • in Polish Adam Mickiewicz University Poznan vol. M.Sc.
    • M. Magnus The development of a metaserver for prediction of protein subcellular localization in bacterial cells and its application to identification of periplasmic proteins in selected Epsilon-proteobacteria in Polish Faculty of Biology 2010 Adam Mickiewicz University Poznan 69 vol. M.Sc.
    • (2010) Faculty of Biology , pp. 69
    • Magnus, M.1
  • 11
    • 0042379959 scopus 로고    scopus 로고
    • Simple consensus procedures are effective and sufficient in secondary structure prediction
    • M. Albrecht, S.C. Tosatto, T. Lengauer, and G. Valle Simple consensus procedures are effective and sufficient in secondary structure prediction Protein Eng. 16 2003 459 462 (Pubitemid 37046142)
    • (2003) Protein Engineering , vol.16 , Issue.7 , pp. 459-462
    • Albrecht, M.1    Tosatto, S.C.E.2    Lengauer, T.3    Valle, G.4
  • 12
    • 24044519380 scopus 로고    scopus 로고
    • MARNA: Multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons
    • DOI 10.1093/bioinformatics/bti550
    • S. Siebert, and R. Backofen MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons Bioinformatics 21 2005 3352 3359 (Pubitemid 41222439)
    • (2005) Bioinformatics , vol.21 , Issue.16 , pp. 3352-3359
    • Siebert, S.1    Backofen, R.2
  • 13
    • 0043123216 scopus 로고    scopus 로고
    • GeneSilico protein structure prediction meta-server
    • DOI 10.1093/nar/gkg557
    • M.A. Kurowski, and J.M. Bujnicki GeneSilico protein structure prediction meta-server Nucleic Acids Res. 31 2003 3305 3307 (Pubitemid 37442145)
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3305-3307
    • Kurowski, M.A.1    Bujnicki, J.M.2
  • 14
    • 0041620242 scopus 로고    scopus 로고
    • BPROMPT: A consensus server for membrane protein prediction
    • DOI 10.1093/nar/gkg554
    • P.D. Taylor, T.K. Attwood, and D.R. Flower BPROMPT: a consensus server for membrane protein prediction Nucleic Acids Res. 31 2003 3698 3700 (Pubitemid 37442226)
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3698-3700
    • Taylor, P.D.1    Attwood, T.K.2    Flower, D.R.3
  • 15
    • 20844435796 scopus 로고    scopus 로고
    • Meta-DP: Domain prediction meta-server
    • DOI 10.1093/bioinformatics/bti445
    • H.K. Saini, and D. Fischer Meta-DP: domain prediction meta-server Bioinformatics 21 2005 2917 2920 (Pubitemid 40862295)
    • (2005) Bioinformatics , vol.21 , Issue.12 , pp. 2917-2920
    • Saini, H.K.1    Fischer, D.2
  • 16
  • 17
    • 34548574787 scopus 로고    scopus 로고
    • Meta-prediction of protein subcellular localization with reduced voting
    • J. Liu, S. Kang, C. Tang, L.B. Ellis, and T. Li Meta-prediction of protein subcellular localization with reduced voting Nucleic Acids Res. 35 2007 e96
    • (2007) Nucleic Acids Res. , vol.35 , pp. 96
    • Liu, J.1    Kang, S.2    Tang, C.3    Ellis, L.B.4    Li, T.5
  • 18
    • 79954434760 scopus 로고    scopus 로고
    • PROlocalizer: Integrated web service for protein subcellular localization prediction
    • K. Laurila, and M. Vihinen PROlocalizer: integrated web service for protein subcellular localization prediction Amino Acids 40 2011 975 980
    • (2011) Amino Acids , vol.40 , pp. 975-980
    • Laurila, K.1    Vihinen, M.2
  • 21
    • 84867684415 scopus 로고    scopus 로고
    • Protein sequence redundancy reduction: Comparison of various methods
    • K. Sikic, and O. Carugo Protein sequence redundancy reduction: comparison of various methods Bioinformation 5 2010 234 239
    • (2010) Bioinformation , vol.5 , pp. 234-239
    • Sikic, K.1    Carugo, O.2
  • 22
    • 3042521098 scopus 로고    scopus 로고
    • Improved prediction of signal peptides: SignalP 3.0
    • DOI 10.1016/j.jmb.2004.05.028, PII S0022283604005972
    • J.D. Bendtsen, H. Nielsen, G. von Heijne, and S. Brunak Improved prediction of signal peptides: SignalP 3.0 J. Mol. Biol. 340 2004 783 795 (Pubitemid 38829638)
    • (2004) Journal of Molecular Biology , vol.340 , Issue.4 , pp. 783-795
    • Bendtsen, J.D.1    Nielsen, H.2    Von Heijne, G.3    Brunak, S.4
  • 23
    • 57249083976 scopus 로고    scopus 로고
    • SPOCTOPUS: A combined predictor of signal peptides and membrane protein topology
    • H. Viklund, A. Bernsel, M. Skwark, and A. Elofsson SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology Bioinformatics 24 2008 2928 2929
    • (2008) Bioinformatics , vol.24 , pp. 2928-2929
    • Viklund, H.1    Bernsel, A.2    Skwark, M.3    Elofsson, A.4
  • 24
    • 2142657817 scopus 로고    scopus 로고
    • A combined transmembrane topology and signal peptide prediction method
    • DOI 10.1016/j.jmb.2004.03.016, PII S0022283604002943
    • L. Kall, A. Krogh, and E.L. Sonnhammer A combined transmembrane topology and signal peptide prediction method J. Mol. Biol. 338 2004 1027 1036 (Pubitemid 38542831)
    • (2004) Journal of Molecular Biology , vol.338 , Issue.5 , pp. 1027-1036
    • Kall, L.1    Krogh, A.2    Sonnhammer, E.L.L.3
  • 25
    • 33645972887 scopus 로고    scopus 로고
    • A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteins
    • M.M. Babu, M.L. Priya, A.T. Selvan, M. Madera, J. Gough, L. Aravind, and K. Sankaran A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteins J. Bacteriol. 188 2006 2761 2773
    • (2006) J. Bacteriol. , vol.188 , pp. 2761-2773
    • Babu, M.M.1    Priya, M.L.2    Selvan, A.T.3    Madera, M.4    Gough, J.5    Aravind, L.6    Sankaran, K.7
  • 26
    • 0041341888 scopus 로고    scopus 로고
    • Prediction of lipoprotein signal peptides in Gram-negative bacteria
    • DOI 10.1110/ps.0303703
    • A.S. Juncker, H. Willenbrock, G. Von Heijne, S. Brunak, H. Nielsen, and A. Krogh Prediction of lipoprotein signal peptides in Gram-negative bacteria Protein Sci. 12 2003 1652 1662 (Pubitemid 36910046)
    • (2003) Protein Science , vol.12 , Issue.8 , pp. 1652-1662
    • Juncker, A.S.1    Willenbrock, H.2    Von Heijne, G.3    Brunak, S.4    Nielsen, H.5    Krogh, A.6
  • 27
    • 78149257874 scopus 로고    scopus 로고
    • Combined prediction of Tat and Sec signal peptides with hidden Markov models
    • P.G. Bagos, E.P. Nikolaou, T.D. Liakopoulos, and K.D. Tsirigos Combined prediction of Tat and Sec signal peptides with hidden Markov models Bioinformatics 26 2010 2811 2817
    • (2010) Bioinformatics , vol.26 , pp. 2811-2817
    • Bagos, P.G.1    Nikolaou, E.P.2    Liakopoulos, T.D.3    Tsirigos, K.D.4
  • 28
    • 67650151451 scopus 로고    scopus 로고
    • Prediction of type III secretion signals in genomes of Gram-negative bacteria
    • M. Lower, and G. Schneider Prediction of type III secretion signals in genomes of Gram-negative bacteria PLoS One 4 2009 e5917
    • (2009) PLoS One , vol.4 , pp. 5917
    • Lower, M.1    Schneider, G.2
  • 30
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
    • DOI 10.1006/jmbi.2000.4315
    • A. Krogh, B. Larsson, G. von Heijne, and E.L. Sonnhammer Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes J. Mol. Biol. 305 2001 567 580 (Pubitemid 33032862)
    • (2001) Journal of Molecular Biology , vol.305 , Issue.3 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    Von Heijne, G.3    Sonnhammer, E.L.L.4
  • 31
    • 3242891271 scopus 로고    scopus 로고
    • ConPred II: A consensus prediction method for obtaining transmembrane topology models with high reliability
    • M. Arai, H. Mitsuke, M. Ikeda, J.X. Xia, T. Kikuchi, M. Satake, and T. Shimizu ConPred II: a consensus prediction method for obtaining transmembrane topology models with high reliability Nucleic Acids Res. 32 2004 W390 W393
    • (2004) Nucleic Acids Res. , vol.32
    • Arai, M.1    Mitsuke, H.2    Ikeda, M.3    Xia, J.X.4    Kikuchi, T.5    Satake, M.6    Shimizu, T.7
  • 32
    • 0030759333 scopus 로고    scopus 로고
    • Prediction of transmembrane α-helices in prokaryotic membrane proteins: The dense alignment surface method
    • M. Cserzo, E. Wallin, I. Simon, G. von Heijne, and A. Elofsson Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method Protein Eng. 10 1997 673 676 (Pubitemid 27332074)
    • (1997) Protein Engineering , vol.10 , Issue.6 , pp. 673-676
    • Cserzo, M.1    Wallin, E.2    Simon, I.3    Von Heijne, G.4    Elofsson, A.5
  • 33
    • 0028211273 scopus 로고
    • A model recognition approach to the prediction of all-helical membrane protein structure and topology
    • D.T. Jones, W.R. Taylor, and J.M. Thornton A model recognition approach to the prediction of all-helical membrane protein structure and topology Biochemistry 33 1994 3038 3049 (Pubitemid 24103366)
    • (1994) Biochemistry , vol.33 , Issue.10 , pp. 3038-3049
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 34
    • 53249092142 scopus 로고    scopus 로고
    • Prediction of membrane protein topology utilizing multiple sequence alignments
    • DOI 10.1023/A:1026353225758
    • B. Persson, and P. Argos Prediction of membrane protein topology utilizing multiple sequence alignments J. Protein Chem. 16 1997 453 457 (Pubitemid 27306548)
    • (1997) Journal of Protein Chemistry , vol.16 , Issue.5 , pp. 453-457
    • Persson, B.1    Argos, P.2
  • 35
    • 48249151108 scopus 로고    scopus 로고
    • OCTOPUS: Improving topology prediction by two-track ANN-based preference scores and an extended topological grammar
    • H. Viklund, and A. Elofsson OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar Bioinformatics 24 2008 1662 1668
    • (2008) Bioinformatics , vol.24 , pp. 1662-1668
    • Viklund, H.1    Elofsson, A.2
  • 36
    • 3242879514 scopus 로고    scopus 로고
    • BOMP: A program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria
    • F.S. Berven, K. Flikka, H.B. Jensen, and I. Eidhammer BOMP: a program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria Nucleic Acids Res. 32 2004 W394 W399
    • (2004) Nucleic Acids Res. , vol.32
    • Berven, F.S.1    Flikka, K.2    Jensen, H.B.3    Eidhammer, I.4
  • 37
    • 25444484398 scopus 로고    scopus 로고
    • TMB-Hunt: An amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins
    • A.G. Garrow, A. Agnew, and D.R. Westhead TMB-Hunt: an amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins BMC Bioinformatics 6 2005 56
    • (2005) BMC Bioinformatics , vol.6 , pp. 56
    • Garrow, A.G.1    Agnew, A.2    Westhead, D.R.3
  • 42
    • 37249058502 scopus 로고    scopus 로고
    • Support Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifs
    • M. Rashid, S. Saha, and G.P. Raghava Support Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifs BMC Bioinformatics 8 2007 337
    • (2007) BMC Bioinformatics , vol.8 , pp. 337
    • Rashid, M.1    Saha, S.2    Raghava, G.P.3
  • 43
    • 77951652612 scopus 로고    scopus 로고
    • Gneg-mPLoc: A top-down strategy to enhance the quality of predicting subcellular localization of Gram-negative bacterial proteins
    • H.B. Shen, and K.C. Chou Gneg-mPLoc: a top-down strategy to enhance the quality of predicting subcellular localization of Gram-negative bacterial proteins J. Theor. Biol. 264 2010 326 333
    • (2010) J. Theor. Biol. , vol.264 , pp. 326-333
    • Shen, H.B.1    Chou, K.C.2
  • 44
    • 46049083380 scopus 로고    scopus 로고
    • Using AdaBoost for the prediction of subcellular location of prokaryotic and eukaryotic proteins
    • B. Niu, Y. Jin, K.Y. Feng, W.C. Lu, Y.D. Cai, and G.Z. Li Using AdaBoost for the prediction of subcellular location of prokaryotic and eukaryotic proteins Mol. Divers. 12 2004 41 45
    • (2004) Mol. Divers. , vol.12 , pp. 41-45
    • Niu, B.1    Jin, Y.2    Feng, K.Y.3    Lu, W.C.4    Cai, Y.D.5    Li, G.Z.6
  • 45
    • 1542400030 scopus 로고    scopus 로고
    • Predicting subcellular localization of proteins using machine-learned classifiers
    • DOI 10.1093/bioinformatics/btg447
    • Z. Lu, D. Szafron, R. Greiner, P. Lu, D.S. Wishart, B. Poulin, J. Anvik, C. Macdonell, and R. Eisner Predicting subcellular localization of proteins using machine-learned classifiers Bioinformatics 20 2004 547 556 (Pubitemid 38344335)
    • (2004) Bioinformatics , vol.20 , Issue.4 , pp. 547-556
    • Lu, Z.1    Szafron, D.2    Greiner, R.3    Lu, P.4    Wishart, D.S.5    Poulin, B.6    Anvik, J.7    Macdonell, C.8    Eisner, R.9
  • 46
    • 16344376554 scopus 로고    scopus 로고
    • A simple statistical method for discriminating outer membrane proteins with better accuracy
    • DOI 10.1093/bioinformatics/bti126
    • M.M. Gromiha, and M. Suwa A simple statistical method for discriminating outer membrane proteins with better accuracy Bioinformatics 21 2005 961 968 (Pubitemid 40467916)
    • (2005) Bioinformatics , vol.21 , Issue.7 , pp. 961-968
    • Gromiha, M.M.1    Suwa, M.2
  • 47
    • 23144463913 scopus 로고    scopus 로고
    • TMBETA-NET: Discrimination and prediction of membrane spanning beta-strands in outer membrane proteins
    • M.M. Gromiha, S. Ahmad, and M. Suwa TMBETA-NET: discrimination and prediction of membrane spanning beta-strands in outer membrane proteins Nucleic Acids Res. 33 2005 W164 W167
    • (2005) Nucleic Acids Res. , vol.33
    • Gromiha, M.M.1    Ahmad, S.2    Suwa, M.3
  • 48
    • 0031336193 scopus 로고    scopus 로고
    • Cost estimation predictive modeling: Regression versus neural network
    • A.E. Smith, and A.K. Mason Cost estimation predictive modeling: regression versus neural network Engineering economist 42 1997 137 162
    • (1997) Engineering Economist , vol.42 , pp. 137-162
    • Smith, A.E.1    Mason, A.K.2
  • 49
    • 33746218840 scopus 로고    scopus 로고
    • Prediction of protein subcellular localization
    • C.S. Yu, Y.C. Chen, C.H. Lu, and J.K. Hwang Prediction of protein subcellular localization Proteins 64 2006 643 651
    • (2006) Proteins , vol.64 , pp. 643-651
    • Yu, C.S.1    Chen, Y.C.2    Lu, C.H.3    Hwang, J.K.4
  • 50
    • 19544388127 scopus 로고    scopus 로고
    • PSLpred: Prediction of subcellular localization of bacterial proteins
    • DOI 10.1093/bioinformatics/bti309
    • M. Bhasin, A. Garg, and G.P. Raghava PSLpred: prediction of subcellular localization of bacterial proteins Bioinformatics 21 2005 2522 2524 (Pubitemid 40731613)
    • (2005) Bioinformatics , vol.21 , Issue.10 , pp. 2522-2524
    • Bhasin, M.1    Garg, A.2    Raghava, G.P.S.3
  • 51
    • 59449110078 scopus 로고    scopus 로고
    • SOSUI-GramN: High performance prediction for sub-cellular localization of proteins in Gram-negative bacteria
    • K. Imai, N. Asakawa, T. Tsuji, F. Akazawa, A. Ino, M. Sonoyama, and S. Mitaku SOSUI-GramN: high performance prediction for sub-cellular localization of proteins in Gram-negative bacteria Bioinformation 2 2008 417 421
    • (2008) Bioinformation , vol.2 , pp. 417-421
    • Imai, K.1    Asakawa, N.2    Tsuji, T.3    Akazawa, F.4    Ino, A.5    Sonoyama, M.6    Mitaku, S.7


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