ICRPfinder: a fast pattern design algorithm for coding sequences and its application in finding potential restriction enzyme recognition sites
1 Department of Biomedical Informatics, Ira A Fulton School Engineering, Arizona State University, Phoenix, AZ 85004, USA
2 Center of Innovations in Medicine, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
3 Center for Infectious Diseases and Vaccinology, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
BMC Bioinformatics 2009, 10:286 doi:10.1186/1471-2105-10-286Published: 11 September 2009
Restriction enzymes can produce easily definable segments from DNA sequences by using a variety of cut patterns. There are, however, no software tools that can aid in gene building -- that is, modifying wild-type DNA sequences to express the same wild-type amino acid sequences but with enhanced codons, specific cut sites, unique post-translational modifications, and other engineered-in components for recombinant applications. A fast DNA pattern design algorithm, ICRPfinder, is provided in this paper and applied to find or create potential recognition sites in target coding sequences.
ICRPfinder is applied to find or create restriction enzyme recognition sites by introducing silent mutations. The algorithm is shown capable of mapping existing cut-sites but importantly it also can generate specified new unique cut-sites within a specified region that are guaranteed not to be present elsewhere in the DNA sequence.