title: ICRPfinder: a fast pattern design algorithm for coding sequences and its application in finding potential restriction enzyme recognition sites.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Biomedical Informatics, Ira A Fulton School Engineering, Arizona State University, Phoenix, AZ 85004, USA. Charles.Li@asu.edu
authors.forename: Chao
authors.initials: C
authors.lastname: Li
authors.forename: Yuhua
authors.initials: Y
authors.lastname: Li
authors.forename: Xiangmin
authors.initials: X
authors.lastname: Zhang
authors.forename: Phillip
authors.initials: P
authors.lastname: Stafford
authors.forename: Valentin
authors.initials: V
authors.lastname: Dinu
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004262:DNA Restriction Enzymes / Q000737:chemistry* / Q000378:metabolism; D030562:Databases, Protein; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D004247:DNA; D004262:DNA Restriction Enzymes