| Calling Sequence
| CodonAlign(seq1,seq2,method,cm)
|
| Parameters
| | Name | Type | Description |
|
| seq1
| string | codon sequence |
| seq2
| string | codon sequence |
| method
| string | the mode of dynamic programming to use |
| cm
| {DayMatrix,list(DayMatrix)} | codon matrices used for alignment |
|
| Return Type
| Alignment |
| Globals
| logPAM1, |
| Synopsis
| CodonAlign does an alignment of two codon sequences using the
similarity scores given in the DayMatrix (of type 'Codon') and the given method.
If a single DayMatrix is given, the alignment is done using it.
If a list of DayMatrix is given, it is understood that the best
CodonPAM matrix be used. Since the introduction of the generic dynamic programming,
CodonAlign is only a wrapper function. It extracts the DNA sequence from an entry
and converts the codon sequence to a character string for the generic Align
function. |
| Examples
| > CodonAlign('AAACCCGGG','AAGCCGGGG', CM);
Alignment('AVq','CWq',30.2765,DM,0,0)
> CodonAlign('AAACCCGGG','AAGCCGGGG',CMS);
Alignment('AVq','CWq',34.3914,DMS[345],79,30984.0898)
|
| See also
| Align, CodonDynProgStrings, CreateCodonMatrices, DayMatrix |