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Table 3 Description of the methods used in the evaluation: For each method, the optimization criteria and the specific parameters are given

From: SplicedFamAlign: CDS-to-gene spliced alignment and identification of transcript orthology groups

Method Optimization criteria Specific parameters
SFA_L sequence similarity splice signal splicing structure tblastx e-value= 10−7
SFA_E   max. number of gaps in extension α = 21 min. PID of aligned segments β = 30
SFA_G   min. PID of aligned segments β = 30
Splign sequence similarity splice signal Default parameters min_exon_identity = 0
SFA_E_ws same as SFA_E with predicted splicing structure