“…The weight matrix method (WMM) is the earliest and most influential one that uses the position-specific compositional biases (Staden, 1984;Tavares et al, 2009). Subsequently, the pattern recognition algorithms, represented by a Bayesian network (Cai et al, 2000), support vector machine (SVM) (Zhang et al, 2006;Baten et al, 2006;Sonnenburg et al, 2007;Asa et al, 2008;Zhang et al, 2009), hidden Markov model (Baten et al, 2007(Baten et al, , 2008Asa et al, 2008;Zhang et al, 2009Zhang et al, , 2010, artificial neural network (Reese et al, 1997;Wang et al, 2009), etc., were successively introduced. A series of special prediction tools were also improved for splice site prediction, such as GeneSplicer (Pertea et al, 2001), DGSplicer (Chen et al, 2005), NNSplice (Reese et al, 1997), SpliceMachine (Kahn et al, 2007), etc.…”