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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 pattern analysis. A plain or FASTA format target DNA sequence can be accepted. Restriction enzymes can be chosen, and also users' pattern sequences can be accepted.
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Figure 2: The GUI of ICRPfinder for specific pattern analysis. A plain or FASTA format target DNA sequence can be accepted. Restriction enzymes can be chosen, and also users' pattern sequences can be accepted.

Mentions: Find all possible potential matches for a specific pattern Figure 2 illustrates the Graphical User Interface (GUI) of the Web application in which users input the target DNA coding sequence and object pattern and configure the parameters. From the menu bar, users can select from two options: (1) find all potential matches for a specific pattern; or (2) find unique matches for all patterns. Below the menu bar, a text box allows for entering and configuring the target DNA coding sequence. Nucleotide sequences in plain text or FASTA format are accepted. The coding sequences (CDS) can be specified and accepted one by one if the input sequence includes not only CDS but also introns or sequences from bacterial vectors. Below the target DNA box, another text box allows the configuration of the object DNA pattern. A list of restriction enzyme recognition sites is pre-loaded as default patterns. User-defined patterns as well as their names can also be accepted.


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 pattern analysis. A plain or FASTA format target DNA sequence can be accepted. Restriction enzymes can be chosen, and also users' pattern sequences can be accepted.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: The GUI of ICRPfinder for specific pattern analysis. A plain or FASTA format target DNA sequence can be accepted. Restriction enzymes can be chosen, and also users' pattern sequences can be accepted.
Mentions: Find all possible potential matches for a specific pattern Figure 2 illustrates the Graphical User Interface (GUI) of the Web application in which users input the target DNA coding sequence and object pattern and configure the parameters. From the menu bar, users can select from two options: (1) find all potential matches for a specific pattern; or (2) find unique matches for all patterns. Below the menu bar, a text box allows for entering and configuring the target DNA coding sequence. Nucleotide sequences in plain text or FASTA format are accepted. The coding sequences (CDS) can be specified and accepted one by one if the input sequence includes not only CDS but also introns or sequences from bacterial vectors. Below the target DNA box, another text box allows the configuration of the object DNA pattern. A list of restriction enzyme recognition sites is pre-loaded as default patterns. User-defined patterns as well as their names can also be accepted.

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