biosed

biosed

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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):

[-sequence] (seqall)

Sequence database USA.

-target (string)

Sequence section to match.

-replace (string)

Replacement sequence section.

[-outseq] (seqout)

Output sequence USA.

Advanced qualifiers:

-delete (boolean)

Delete the target sequence sections.