Numerical characterization of DNA sequences based on digital signal method

Zhang, Qi; Qi, Xiao-Qin

doi:10.1016/j.compbiomed.2009.01.009

Cited by 17 publications

(14 citation statements)

References 21 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It can be used to analyze both short and long DNA sequences. As an application, this method is tested on the exon-1 coding sequences of β -globin for 11 species and the results are consistent with what have been reported previously [5, 9, 12, 14, 15], which prove the utility of this new method.…”

Section: Introductionsupporting

confidence: 85%

See 1 more Smart Citation

Numerical Characterization of DNA Sequence Based on Dinucleotides

Fuller

et al. 2012

The Scientific World Journal

View full text Add to dashboard Cite

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.

show abstract

Section: Introductionsupporting

confidence: 85%

“…There are also approaches which could arrive a mathematical representation of DNA sequences by nongraphical ways, see [11–13]. And more recently, a new representation based on symbolic dynamics [14] and a new representation based on digital signal method [15] are also illustrated.…”

Section: Introductionmentioning

confidence: 99%

Numerical Characterization of DNA Sequence Based on Dinucleotides

Fuller

et al. 2012

The Scientific World Journal

View full text Add to dashboard Cite

show abstract

“…However, the related computation of these matrices becomes complex when DNA sequence is long. Recently, Bielinska-Waz, [25,26] Qi, [27] and Zhang [28] propose some new descriptors. These descriptors are proved to be useful and used to resolve the problem for similarity comparison of sequences.…”

Section: Introductionmentioning

confidence: 99%

Using Huffman coding method to visualize and analyze DNA sequences

Zhang

2011

J Comput Chem

Self Cite

View full text Add to dashboard Cite

On the basis of the Huffman coding method, we propose a new graphical representation of DNA sequence. The representation can avoid degeneracy and loss of information in the transfer of data from a DNA sequence to its graphical representation. Then a multicomponent vector from the representation is introduced to characterize quantitatively DNA sequences. The components of the vector are derived from the graphical representation of DNA primary sequence. The examination of similarities and dissimilarities among the complete coding sequences of β-globin gene of 11 species and six ND6 proteins shows the utility of the scheme.

show abstract

“…In general, it is difficult to come to a conclusion by analyzing DNA sequence with great deals of characters, especially when the sequence is long. In this fields, statistical method has become an important means in biological information processing, such as frequency, correlation analysis, Markov chain, neural network, Bayesian statistics, information entropy [4][5][6].…”

Section: Preprocessing Of Ha Gene Sequencementioning

confidence: 99%

Evolution analysis for HA gene of human influenza A H3N2 virus (1990 – 2013)

Jin

Zhang

2014

2014 8th International Conference on Systems Biology (ISB)

Self Cite

View full text Add to dashboard Cite

Human influenza A virus is an important pathogen which threatens the health of human in a long time. The mutation study of HA gene is the most important. Here we investigate the evolution characteristics of HA gene of H3N2 influenza virus from 1990 to 2013. Numerical mapping and PCA clustering analysis are applied to the gene evolution analysis. The clustering diagram by MATLAB represents the mapping of HA gene in 2D space. The first two principal components account for 78.48% by PCA analysis. And the points are clustered into three parts, 1990~1999, 2000~2005 and 2006~2013. However, there is no obvious interval among them. Then we show the graphical representation of HA gene sequences according to the emerging time of isolates and different continents. Results show that during 1990 to 2013 human influenza A H3N2 virus has been evoluting gradually. There was not large genetic recombination. Even so, it is necessary to continuously monitor the human influenza A (H3N2) viruses.

show abstract

Numerical characterization of DNA sequences based on digital signal method

Cited by 17 publications

References 21 publications

Numerical Characterization of DNA Sequence Based on Dinucleotides

Numerical Characterization of DNA Sequence Based on Dinucleotides

Using Huffman coding method to visualize and analyze DNA sequences

Evolution analysis for HA gene of human influenza A H3N2 virus (1990 – 2013)

Contact Info

Product

Resources

About

Numerical characterization of DNA sequences based on digital signal method

Cited by 17 publications

References 21 publications

Numerical Characterization of DNA Sequence Based on Dinucleotides

Numerical Characterization of DNA Sequence Based on Dinucleotides

Using Huffman coding method to visualize and analyze DNA sequences

Evolution analysis for HA gene of human influenza A H3N2 virus (1990 &#x2013; 2013)

Contact Info

Product

Resources

About

Evolution analysis for HA gene of human influenza A H3N2 virus (1990 – 2013)