biosed is a simple sequence editing utility that searches for a target subsequence in one or more input sequences and replaces it with a specified second subsequence (or optionally just deletes the found target subsequence). biosed was inspired by the useful Unix utility sed.
Here is a sample session with biosed that replaces all "T's" with "U's" to create an RNA sequence:
% biosed em:hsfau hsfau.rna -target T -replace U
Replace all "RGD" protein motifs with "XXRGDXX":
% biosed sw:A4M1_HUMAN A4M1_HUMAN.pep -target RGD -replace XXRGDXX
Mandatory qualifiers (bold if not always prompted):