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Finds restriction sites that can be engineered into a gene without changing the amino acid sequence



Short Description

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Seqsearcher takes a polypeptide sequence and returns positions where silent mutations can be introduced to create restriction sites. Since it can't tell what the real DNA sequence is, it will also find real restriction sites. This is useful for generating cloning sites for cassette mutagenesis[1]. Cassette mutagenesis based on cloning between restriction sites has largely been superceded by PCR methods, but the software is available.

Because the technique is not widely used anymore, further development of SeqSearcher is not being actively pursued.


Seqsearcher can be run via a web form at


The current version of SeqSearcher is a php script and is largely platform independent. The code can be downloaded here.

User notes

See Also

Similar functionality is available from other sequence analysis packages.


See Help:References for how to manage references in EcoliWiki.

  1. Reidhaar-Olson, JF et al. (1991) Random mutagenesis of protein sequences using oligonucleotide cassettes. Meth. Enzymol. 208 564-86 PubMed