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Using position specific scoring matrix and auto covariance ..:

Xiao, Rong-Quan ; Guo, Yan-Zhi ; Zeng, Yu-Hong...
Journal of Biomedical Science and Engineering.  2 (2009)  1 - p. 51-56 , 2009
Link: https://doi.org/10.4236/jbise.2009.21009