triplex.score.table: Get default scoring tables
In triplex: Search and visualize intramolecular triplex-forming sequences in DNA

Description Usage Details Value Note Author(s) References See Also Examples

The triplex.score.table function returns default scoring tables for parallel and antiparallel triplex types.

1	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.

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 (lambda, mu and 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

triplex.group.table triplex.search, TriplexViews, triplex.diagram, triplex.3D, triplex.alignment