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Objective: The existing informatics applications are specialized in particular aspects of the enzymatic restriction analysis of nucleotides sequences. In order to design an application that fulfills different needs of the investigation in restriction enzyme analysis, I have developed SQRestriction (SQR), a suite that compiles several utilities.
Methods: I applied object-oriented programming to set algorithms in C++ that compare the differences or similarities in the restriction sites of orthologous genes or in nucleotide sequences with single nucleotide polymorphisms, insertions or deletions.
Results: SQR is mainly a tool for the analysis of restriction fragment length polymorphisms but it has also other applications such as cloning of DNA; I demonstrate those functions in examples of different types of nucleotide sequences. I conducted a comparative analysis between SQR and existing software in the web; the main difference is that SQR is a suite of different applications that analyzes either one, two or multiple sequences of nucleotides.
Conclusion: I conclude that SQR is a competitive application since it offers differential features that are useful for academics and in laboratories of molecular biology. The SQRestriction software is open access at http://www2.uah.es/biologia_celular/JPM/SQR/SQR.html
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