Table 2 Description of the five methods considered in the experiment
From: Aligning coding sequences with frameshift extension penalties
Method | Alignment approach and specific parameters | FS initiation cost | Other parameters |
|---|---|---|---|
fse | Present approach \({\texttt{fs}}\_{\texttt{extend}}\_{\texttt{cost}} =\) \(\,-1; -0.5; -0.2\) | \({\texttt{fs}}\_{\texttt{open}}\_{\texttt{cost}} =\) −10; −20; −30 | \({\texttt{AA}} \quad {\texttt{gap}}\_{\texttt{open}}\_{\texttt{cost}} = -11\) \({\texttt{AA}} \quad {\texttt{gap}}\_{\texttt{cost}} = -1\) \(s_{aa} =\,{\texttt{BLOSUM62}} \quad {\texttt{matrix}}\) \(s_{an} =\,\) +1/-1 match/mismatch |
fse0 | Present approach \({\texttt{fs}}\_{\texttt{extend}}\_{\texttt{cost}} = 0\) | ||
macse_p | Ranwez et al. [18] \({\texttt{stop}}\_{\texttt{cost}} = -100\) | ||
needleprot | NW [24] at AA level | Not applicable | |
needlenuc | NW [24] at NT level | Not applicable | \({\texttt{NT}} \quad {\texttt{gap}}\_{\texttt{open}}\_{\texttt{cost}} = -5\) |
\({\texttt{NT}} \quad {\texttt{gap}}\_{\texttt{cost}} = -2\) | |||
\(s_{an} =\) +2/-3 | |||
match/mismatch |