microseq (version 2.1.6)

iupac2regex: Ambiguity symbol conversion

Description

Converting DNA ambiguity symbols to regular expressions, and vice versa.

Usage

iupac2regex(sequence)
regex2iupac(sequence)

Value

A string where the ambiguity symbol has been replaced by a regular expression (iupac2regex) or a regular expression has been replaced by an ambiguity symbol (regex2iupac).

Arguments

sequence

Character vector containing DNA sequences.

Author

Lars Snipen.

Details

The DNA alphabet may contain ambiguity symbols, e.g. a W means either A or T. When using a regular expression search, these letters must be replaced by the proper regular expression, e.g. W is replaced by [AT] in the string. The iupac2regex makes this translation, while regex2iupac converts the other way again (replace [AT] with W).

Examples

iupac2regex("ACWGT")
regex2iupac("AC[AG]GT")