This function computes best triplex alignment.
Similarly to other DNA multiple sequence alignments the output of the
triplex.alignment method is stored as
object. This object consists of four sequences:
sequences representing 5' to 3' and 3' to 5' DNA strand of detected triplex;
one of the
para-minus sequence representing the third triplex strand aligned to
minus strand in
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.
TriplexViews object is required to provide additional
algorithm options (see
triplex.search). These are used for
proper computation of triplex alignment.
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