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

Li C, Li Y, Zhang X, Stafford P, Dinu V - BMC Bioinformatics (2009)

Bottom Line: ICRPfinder is applied to find or create restriction enzyme recognition sites by introducing silent mutations.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biomedical Informatics, Ira A Fulton School Engineering, Arizona State University, Phoenix, AZ 85004, USA. Charles.Li@asu.edu

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.

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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Related in: MedlinePlus

The GUI of ICRPfinder for specific position analysis. The specific position can be accepted. All patterns, including restriction enzymes and user's patterns are analyzed.
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Figure 4: The GUI of ICRPfinder for specific position analysis. The specific position can be accepted. All patterns, including restriction enzymes and user's patterns are analyzed.

Mentions: Figure 4 illustrates the GUI by which users can analyze a DNA sequence around a specific position. There are two main differences between this and Figure 2. The first is that only the sequence within a short range of the specified position is displayed. The range is expected to be no more than 20 nucleotides since recognition sites are normally only several nucleotides in length, but the range is not limited to that size so as not to restrict the possible use of this tool for other purposes. The second difference is that patterns do not need to be selected, since all patterns are analyzed. This function is useful to find all patterns which are located only around a specific position and nowhere else in the target coding sequence. As only one possible matched site is found or created, the other parts of the target coding sequence will be unaffected.


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

Li C, Li Y, Zhang X, Stafford P, Dinu V - BMC Bioinformatics (2009)

The GUI of ICRPfinder for specific position analysis. The specific position can be accepted. All patterns, including restriction enzymes and user's patterns are analyzed.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2746817&req=5

Figure 4: The GUI of ICRPfinder for specific position analysis. The specific position can be accepted. All patterns, including restriction enzymes and user's patterns are analyzed.
Mentions: Figure 4 illustrates the GUI by which users can analyze a DNA sequence around a specific position. There are two main differences between this and Figure 2. The first is that only the sequence within a short range of the specified position is displayed. The range is expected to be no more than 20 nucleotides since recognition sites are normally only several nucleotides in length, but the range is not limited to that size so as not to restrict the possible use of this tool for other purposes. The second difference is that patterns do not need to be selected, since all patterns are analyzed. This function is useful to find all patterns which are located only around a specific position and nowhere else in the target coding sequence. As only one possible matched site is found or created, the other parts of the target coding sequence will be unaffected.

Bottom Line: ICRPfinder is applied to find or create restriction enzyme recognition sites by introducing silent mutations.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biomedical Informatics, Ira A Fulton School Engineering, Arizona State University, Phoenix, AZ 85004, USA. Charles.Li@asu.edu

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.

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.

Show MeSH
Related in: MedlinePlus