DNAPatternAlphabet {Biostrings}R Documentation

functions to create DNA and RNA pattern alphabets

Description

The function DNAAlphabet returns an alphabet consisting of standard patterns used in DNA sequences.

The function RNAAlphabet returns an alphabet consisting of standard patterns used in RNA sequences.

Usage

DNAPatternAlphabet()
RNAPatternAlphabet()

Value

An object of class "BioPatternAlphabet". See BioPatternAlphabet-class for details.

Memebers of the pattern alphabets

In the table below, we provide the letters from the base DNA alphabet that are matched by the added letters in the DNA pattern alphabet. The corresponding table for RNA is identical except for the substitution of ‘U’ for ‘T’.

‘N’ matches ‘A’, ‘C’, ‘G’, ‘T’
‘B’ matches ‘C’, ‘G’, ‘T’
‘D’ matches ‘A’, ‘G’, ‘T’
‘H’ matches ‘A’, ‘C’, ‘T’
‘K’ matches ‘G’, ‘T’
‘M’ matches ‘A’, ‘C’
‘R’ matches ‘A’, ‘G’
‘S’ matches ‘C’, ‘G’
‘V’ matches ‘A’, ‘C’, ‘G’
‘W’ matches ‘A’, ‘T’
‘Y’ matches ‘C’, ‘T’

Author(s)

Saikat DebRoy

See Also

DNAAlphabet, RNAAlphabet

Examples

DNAPatternAlphabet()
RNAPatternAlphabet()

[Package Biostrings version 1.4.0 Index]