Journal of Biological Sciences1727-30481812-5719Asian Network for Scientific Information10.3923/jbs.2005.795.800ZakiNazar DerisSafaai 6200556This study introduces a simple method based on representing protein sequence by fix dimensions of the length three. We present hidden Markov model combining scores method. Three scoring algorithms are combined to represent protein sequence of amino acids for better remote homology detection. We tested the method on the SCOP version 1.37 dataset. The results show that, with such a simple representation, we are able to achieve superior performance to previously presented protein homology detection methods while achieving better computational efficiency.]]>Smith, T.F. and M.S. Waterman,1981147195197Pearson, W. R.,19901836398Altschul, S.F., W. Gish, W. Miller, E.W. Myers and D.J. Lipman,1990215403410Gribskov. M., R. Luthy and D. Eisenberg,19901831461595. Baldi, P., Y. Chauvin, T. Hunkapiller and M.A. Mcclure,19949110591063Krogh, A., M. Brown, I.S. Mian, K. Sjolander and D. Haussler,199423515011531Altschul, S.F., T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller and D.J. Lipman,19972533893402Karplus, K., C. Barrett and R. Hughey, 199814846856Jaakkola, T., M. Diekhans and D. Haussler,2000795114Vapnik, V.N.,19981st Edn.,Cristianini, N. and J. Shawe-Taylor,2000Leslie, C., E. Eskin, J. Weston and W. Noble, 200420467476Barrett, C., R. Hughey and K. Karplus,199713191199Liao, L. and W.S. Noble, 200310857868Logan, B., P. Moreno, B. Suzek, Z. Weng and S. Kasif,2001Jaakkola, T., M. Diekhans and D. Haussler,1999pp: 149-158.pp: 149-158.Murzin, A.G., S.E. Brenner, T. Hubbard and C. Chothia,1995247536540Swets, J.A.,198827012851293Salzberg, S.L., 19971317328Henikoff, S. and J.G. Henikoff, 19976698705Shimshoni, Y. and N. Intrator, 19984611941201Merz, C., 1999363358