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 | |