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

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.Restriction enzymes and methylase are components of a bacterial mechanism aimed at resisting attack from bacteriophages and removing foreign viral DNA sequences. A restriction enzyme cuts a DNA molecule and forms a sticky or blunt end at each side of the incision site without damaging the nitrogenous bases. A DNA ligase can then splice a cut end to that of another DNA molecule. Each restriction endonuclease is an enzyme that recognizes a specific DNA sequence and cuts the DNA molecule at a particular position in relation to the recognition sequence, producing a blunt or overhanging end, depending upon the enzyme chosen. While restriction enzymes typically recognize specific short DNA sequences, the genetic code is redundant, with most amino acids being represented by more than one codon. Therefore, with creative use of sequence modifications, and use of synonymous codons, one can create restriction sites without changing the precise amino acid sequence coded for.A DNA sequence can be synthesized by assembling short synthetic oligonucleotides using PCR amplification. Using this approach, several oligonucleotides with overlapping end sequences can be assembled into a whole DNA sequence [1]. DNA synthesis using this PCR-based ligation method, however, has some limitations. For exam