| Calling Sequence
| Alignment(Seq1,Seq2,Score,DayMatrix,PamDistance,PamVariance,modes)
|
| Parameters
| | Name | Type | Description |
|
| Seq1
| string | the first protein or DNA sequence |
| Seq2
| string | the second protein or DNA sequence |
| Score
| numeric | score of the alignment |
| DayMatrix
| DayMatrix | Dayhoff matrix used |
| PamDistance
| numeric | estimate of the PAM distance or 0 |
| PamVariance
| numeric | variance of the PAM distance or 0 |
| modes
| set(string) | optional modes of alignment |
|
| Selectors
| | Name | Type | Description |
|
| Identity
| numeric | fraction identical positions (0..1) |
| Length1
| posint | length of Seq1 |
| Length2
| posint | length of Seq2 |
| Offset1
| integer | database offset of Seq1 |
| Offset2
| integer | database offset of Seq2 |
| PamNumber
| numeric | synonym of PamDistance |
| Sim
| numeric | synonym of Score |
|
| Methods
| HTMLC, LaTeXC, lprint, Match, print, Rand, select, Sequence, string |
| Synopsis
| An Alignment stores the information of a pairwise
alignment between two sequences (protein or DNA).
It replaces the Match structure, which is now obsolete.
If the mode for the alignment is just Local or unknown, it is
omitted, otherwise it is a set with one of {Local,Global,CFE,Shake}
and optionally NoSelf. |
| See also
| Align, CalculateScore, DynProgScore, DynProgStrings, EstimatePam, MAlignment |