| Calling Sequence
| TotalAlign(m,DM,goal)
|
| Parameters
| | Name | Type | Description |
|
| m
| Match | a Match |
| DM
| DayMatrix | a Dayhoff Matrix |
| goal
| numeric | a threshold value |
|
| Return Type
| list(Match) |
| Synopsis
| The TotalAlign function implements the Smith-Waterman
algorithm SmithW81 with an extension to find all independent local
alignments of the complete sequences of 'm' reaching a score of at
least 'goal'. The alignments are computed at PAM distance defined
by the similarity matrix DM. |
| Examples
| |
| See also
| CreateDayMatrices, MAlign |