TY - JOUR
T1 - ICRPfinder
T2 - A fast pattern design algorithm for coding sequences and its application in finding potential restriction enzyme recognition sites
AU - Li, Chao
AU - Li, Yuhua
AU - Zhang, Xiangmin
AU - Stafford, Phillip
AU - Dinu, Valentin
N1 - Funding Information:
The authors would like to thank Jack Emery for comments that improved this manuscript. This work was supported by start-up fund from ASU to Stephen Albert Johnston.
PY - 2009/9/11
Y1 - 2009/9/11
N2 - 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. Conclusion: 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.
AB - 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. Conclusion: 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.
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U2 - 10.1186/1471-2105-10-286
DO - 10.1186/1471-2105-10-286
M3 - Article
C2 - 19747395
AN - SCOPUS:70349742594
SN - 1471-2105
VL - 10
SP - 286
JO - BMC bioinformatics
JF - BMC bioinformatics
M1 - 286
ER -