triplex.score.table function returns default scoring tables
for parallel and antiparallel triplex types.
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
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
List of two matrixes, one for parallel triplex types and the other one for antiparallel.
If you modify the scoring tables,
you should consider changing also default P-value constants (
rn), because these are valid just for the default scoring tables.
Tomas Martinek, Jiri Hon
Lexa, M., Martinek, T., Burgetova, I., Kopecek, D., Brazdova, M.: A dynamic programming algorithm for identification of triplex-forming sequences, In: Bioinformatics, Vol. 27, No. 18, 2011, Oxford, GB, p. 2510-2517, ISSN 1367-4803
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