Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Open Badges Software

ICRPfinder: a fast pattern design algorithm for coding sequences and its application in finding potential restriction enzyme recognition sites

Chao Li12*, Yuhua Li3, Xiangmin Zhang3, Phillip Stafford2 and Valentin Dinu1

Author Affiliations

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

For all author emails, please log on.

BMC Bioinformatics 2009, 10:286  doi:10.1186/1471-2105-10-286

Published: 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.


ICRPfinder is a powerful tool for finding or creating specific DNA patterns in a given target coding sequence. ICRPfinder finds or creates patterns, which can include restriction enzyme recognition sites, without changing the translated protein sequence. ICRPfinder is a browser-based JavaScript application and it can run on any platform, in on-line or off-line mode.