Numerical Characterization of DNA Sequence Based on Dinucleotides
Sequence comparison is a primary technique for the analysis of DNA sequences. In order to make quantitative comparisons, one devises mathematical descriptors that capture the essence of the base composition and distribution of the sequence. Alignment methods and graphical techniques (where each sequ...
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| Format: | Article |
| Language: | English |
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Wiley
2012-01-01
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| Series: | The Scientific World Journal |
| Online Access: | http://dx.doi.org/10.1100/2012/104269 |
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| author | Xingqin Qi Edgar Fuller Qin Wu Cun-Quan Zhang |
| author_facet | Xingqin Qi Edgar Fuller Qin Wu Cun-Quan Zhang |
| author_sort | Xingqin Qi |
| collection | DOAJ |
| description | Sequence comparison is a primary technique for the analysis of DNA sequences. In order to make quantitative comparisons, one devises mathematical descriptors that capture the essence of the base
composition and distribution of the sequence. Alignment methods and graphical techniques (where each sequence is represented by a curve in high-dimension Euclidean space) have been used popularly
for a long time. In this contribution we will introduce a new nongraphical and nonalignment approach based on the frequencies of the dinucleotide XY in DNA sequences. The most important feature of this method is that it not only identifies adjacent XY pairs but also nonadjacent XY ones where X and Y are separated by some number of nucleotides. This methodology preserves information in DNA sequence that is ignored by other methods. We test our method on the coding regions of exon-1 of β–globin for 11 species, and the utility of this new method is demonstrated. |
| format | Article |
| id | doaj-art-92220077aac847ff86d955cbb0f20cfe |
| institution | Kabale University |
| issn | 1537-744X |
| language | English |
| publishDate | 2012-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | The Scientific World Journal |
| spelling | doaj-art-92220077aac847ff86d955cbb0f20cfe2025-02-03T01:20:50ZengWileyThe Scientific World Journal1537-744X2012-01-01201210.1100/2012/104269104269Numerical Characterization of DNA Sequence Based on DinucleotidesXingqin Qi0Edgar Fuller1Qin Wu2Cun-Quan Zhang3School of Mathematics and Statistics, Shandong University at Weihai, Weihai 264209, ChinaDepartment of Mathematics, West Virginia University, Morgantown, WV 26506, USASchool of IOT Engineering, Jiangnan University, Wuxi 214122, ChinaDepartment of Mathematics, West Virginia University, Morgantown, WV 26506, USASequence comparison is a primary technique for the analysis of DNA sequences. In order to make quantitative comparisons, one devises mathematical descriptors that capture the essence of the base composition and distribution of the sequence. Alignment methods and graphical techniques (where each sequence is represented by a curve in high-dimension Euclidean space) have been used popularly for a long time. In this contribution we will introduce a new nongraphical and nonalignment approach based on the frequencies of the dinucleotide XY in DNA sequences. The most important feature of this method is that it not only identifies adjacent XY pairs but also nonadjacent XY ones where X and Y are separated by some number of nucleotides. This methodology preserves information in DNA sequence that is ignored by other methods. We test our method on the coding regions of exon-1 of β–globin for 11 species, and the utility of this new method is demonstrated.http://dx.doi.org/10.1100/2012/104269 |
| spellingShingle | Xingqin Qi Edgar Fuller Qin Wu Cun-Quan Zhang Numerical Characterization of DNA Sequence Based on Dinucleotides The Scientific World Journal |
| title | Numerical Characterization of DNA Sequence Based on Dinucleotides |
| title_full | Numerical Characterization of DNA Sequence Based on Dinucleotides |
| title_fullStr | Numerical Characterization of DNA Sequence Based on Dinucleotides |
| title_full_unstemmed | Numerical Characterization of DNA Sequence Based on Dinucleotides |
| title_short | Numerical Characterization of DNA Sequence Based on Dinucleotides |
| title_sort | numerical characterization of dna sequence based on dinucleotides |
| url | http://dx.doi.org/10.1100/2012/104269 |
| work_keys_str_mv | AT xingqinqi numericalcharacterizationofdnasequencebasedondinucleotides AT edgarfuller numericalcharacterizationofdnasequencebasedondinucleotides AT qinwu numericalcharacterizationofdnasequencebasedondinucleotides AT cunquanzhang numericalcharacterizationofdnasequencebasedondinucleotides |