triplex.score.table: Get default scoring tables

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

View source: R/triplex.table.R

Description

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

Usage

1

Details

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.

Value

List of two matrixes, one for parallel triplex types and the other one for antiparallel.

Note

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.

Author(s)

Tomas Martinek, Jiri Hon

References

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

See Also

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

Examples

1

triplex documentation built on Nov. 17, 2017, 1:37 p.m.