triplex.group.table: Get default isogroup tables

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

View source: R/triplex.table.R

Description

The triplex.group.table function returns default isogroup tables for parallel and antiparallel triplex types.

Usage

1

Details

This function is used by triplex.search function to get default isogroup tables. These tables correspond exactly with Table 1 published in (Lexa, 2011) and they represent the isomorphic groups of triplets.

As a common triplet structure is H.WC:WC, to customize isogroup tables just use H as a row index, WC as a column index, then set desired group number and pass such modified tables through group_table option of triplex.search interface.

Value

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

Note

If you modify the isogroup tables, you should consider changing also default P-value constants (lambda, mu and rn), because these are valid just for the default isogroup 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.score.table triplex.search, TriplexViews, triplex.diagram, triplex.3D, triplex.alignment

Examples

1

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