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Based on the position information and numbers of k-words, a method is proposed to compare genetic sequences and infer evolutionary relationship. In this study a characteristic vector whose elements are the average distances from the beginning of the k-word is introduced to represent DNA sequences. The approach has one to one correspondence between DNA sequences and vectors. In the end, we choose 48...
DNA sequences are often found to be composed of locally homogeneous segments that are functionally important. Most sequence comparison methods do not consider such a compositional property. We introduce a new method that takes this issue into consideration. With our method, the information of a DNA sequence is first transformed into a multi-order transition matrix (MTM); the resulting matrices are...
Phylogenic analysis relies on alignment of related sequences from different species to obtain the distances between these species. The quality of the alignment and the distance measure would depend on the alignment parameters that are used. In this work, we propose to use Relative Complexity Measure (RCM) to find the distances between the sequences which is not a parameter dependent measure. We used...
A phylogenetic or evolutionary tree is constructed from a set of species or DNA sequences and depicts the relatedness between the sequences. Predictions of future sequences in a phylogenetic tree are important for a variety of applications including drug discovery, pharmaceutical research and disease control. In this work, we predict future DNA sequences in a phylogenetic tree using cellular automata...
ZmPP2C was a protein phosphatase 2C gene that we cloned from maize roots. It is an important type of protein phosphatase family. AlignX is a software which can compare homology of many proteins or nucleic acids and search homologous fragments or different bases in high similarity sequences. This paper makes use of the AlignX program to visualize and analyze DNA sequences of ZmPP2C comparing with other...
The diversity of life is staggering which is apparent not only in the large number of species, but also in their heterogeneity. Species share commonalities based on their physical appearance, but the intrinsic similarities lies within their DNA sequences which point towards relationships of evolutionary descent. In the proposed research, the authors have analyzed the phylogenetic relationships between...
The Maximum Parsimony (MP) problem aims at reconstructing a phylogenetic tree from DNA sequences while minimizing the number of genetic transformations. To solve this NP-complete problem, heuristic methods have been developed, often based on local search. In this paper, we focus on the influence of the neighborhood relations. After analyzing the advantages and drawbacks of the well-known Nearest Neighbor...
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