文章基本信息

标题：DNA representation based on ladder like structure property of DNA sequence double Helix
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作者：Archana Verma ; R.K.Singh
期刊名称：International Journal of Computer Science and Information Technologies
电子版ISSN：0975-9646
出版年度：2012
卷号：3
期号：4
页码：4596-4598
出版社：TechScience Publications
摘要：Biological sequences play a major role in molecular and computational biology.DNA sequence representation remains as one of the critical steps in the analysis of relationships between species. There are several 2- D and 3-D graphical representation methods for DNA sequences. We have introduced a tabular method for representing DNA sequences which will decreases the degeneracy problem occurred in earlier methods. Now we want to utilized our tabular approach for representation. This approach captures the essence of the base composition and distribution of the sequence. The choice of the tabular representation technique for a DNA sequence affects how well its biological properties can be reflected in the graphical domain for visualization and analysis of the characteristics of special regions of interest within the DNA sequence. In this contribution, we take the DNA sequence double helix into account, and make use of an earlier introduced tabular method for representing each DNA sequence based on the frequencies of bases it contains. Then we convert this tabular information to construct a ladder like structure. We are using the double helix property of DNA sequence and its resemblance with ladder like structure. Then an algorithm for preparing a DNA ladder is presented which will utilize the tabular representation of DNA sequences. The method is very simple and fast, and it can be used to analyze both short and long DNA sequences. The utility of this method is tested on Goat alanine β -globin 86 bases. This paper also presents a summary of various DNA graphical representation methods and their applications in envisaging and analyzing long DNA sequences. A discussion on the comparative merits and demerits of the various methods and conclusions has also been included.
关键词：Biological sequences play a major role in;molecular and computational biology.DNA sequence;representation remains as one of the critical steps in the;analysis of relationships between species. There are several 2-;D and 3-D graphical representation methods for DNA;sequences. We have introduced a tabular method for;representing DNA sequences which will decreases the;degeneracy problem occurred in earlier methods. Now we;want to utilized our tabular approach for representation. This;approach captures the essence of the base composition and;distribution of the sequence. The choice of the tabular;representation technique for a DNA sequence affects how well;its biological properties can be reflected in the graphical;domain for visualization and analysis of the characteristics of;special regions of interest within the DNA sequence. In this;contribution; we take the DNA sequence double helix into;account; and make use of an earlier introduced tabular;method for representing each DNA sequence based on the;frequencies of bases it contains. Then we convert this tabular;information to construct a ladder like structure. We are using;the double helix property of DNA sequence and its;resemblance with ladder like structure. Then an algorithm for;preparing a DNA ladder is presented which will utilize the;tabular representation of DNA sequences. The method is very;simple and fast; and it can be used to analyze both short and;long DNA sequences. The utility of this method is tested on;Goat alanine β -globin 86 bases. This paper also presents a;summary of various DNA graphical representation methods;and their applications in envisaging and analyzing long DNA;sequences. A discussion on the comparative merits and;demerits of the various methods and conclusions has also been;included.