triplex.alignment {triplex} | R Documentation |
This function computes best triplex alignment.
triplex.alignment(triplex)
triplex |
|
Similarly to other DNA multiple sequence alignments the output of the
triplex.alignment
method is stored as DNAStringSet
object. This object consists of four sequences: plus
and minus
sequences representing 5' to 3' and 3' to 5' DNA strand of detected triplex;
one of the anti-plus
, anti-minus
, para-plus
or
para-minus
sequence representing the third triplex strand aligned to
plus
or minus
strand in antiparallel
or parallel
fashion; and finally loop
sequence representing unpaired loop.
Please note that all eight triplex types shown in following figure can be represented using four types of alignments, because each alignment can correspond to triplex detected either on forward or reverse DNA strand.
The input TriplexViews
object is required to provide additional
algorithm options (see triplex.search
). These are used for
proper computation of triplex alignment.
Instance of DNAStringSet
object.
Jiri Hon
triplex.diagram
,
triplex.3D
,
triplex.search
seq <- DNAString("GGAAAGCAATGCCAGGCAGGG") t <- triplex.search(seq, min_score=10, p_value=1) triplex.alignment(t[1])