triplex.score.table function returns default scoring tables
for parallel and antiparallel triplex types.
triplex.score.table()This function is used by triplex.search function to get
default scoring tables. These tables correspond exactly with Table 1 published
in (Lexa, 2011) and they represent the strength of Hoogsteen bonds between
thirdstrand nucleotide (row index) and a nucleotide from duplex (column index).
As a common triplet structure is H.WC:WC, to customize scoring tables
just use H as a row index, WC as a column index, then set desired score value and
pass such modified tables through score_table option of triplex.search
interface.
Please keep in mind that for a mismatch (no bond at all) special value -9 is used.
If you want to change mismatch penalization, please use mis_pen option of
triplex.search function.
triplex.group.table
triplex.search,
TriplexViews,
triplex.diagram,
triplex.3D,
triplex.alignment