| Calling Sequence
| EstimatePam(s1,s2,days)
|
| Parameters
| | Name | Type | Description |
|
| s1
| string | |
| s2
| string | |
| days
| array(DayMatrix) | |
|
| Return Type
| [Score,PamDistance,PamVariance] |
| Synopsis
| Calculates the similarity score, Pam distance
and Pam variance for the alignment defined by s1 and s2. Notice
that s1 and s2 are taken as aligned already, that is, they are
not re-aligned. If s1 and s2 need to be aligned,
use DynProgStrings first.
The estimation of the Pam distance and variance is normally done
by Align when given an array of Dayhoff matrices.
If the the estimated distance is lower than 0.1 pam,
the estimate is also computed by expected values (the computation
of distances by maximum likelihood becomes less accurate).
This second estimate is stored in the global variable
ExpectedPamDistance.
The computation of the PamDistance by maximum likelihood
(exactly, not just for an existing DM in days)
is stored in the global variable MLPamDistance. |
| Examples
| > EstimatePam('CITKLFDGDQVLY', Mutate('CITKLFDGDQVLY', 100), DMS);
[73.1848, 61, 822.4780]
|
| See also
| Align, CalculateScore, DynProgStrings, EstimateCodonPAM, EstimateSynPAM |