A Burrows-Wheeler Transform Based Method for DNA Sequence Comparison
Chun Li,
Huan Liu,
Junhong Liu,
Yuping Qin,
Zhifu Wang
Issue:
Volume 2, Issue 3, June 2014
Pages:
33-37
Received:
22 April 2014
Accepted:
15 May 2014
Published:
30 May 2014
Abstract: Burrows-Wheeler Transform (BWT) is an extremely useful tool for textual lossless data compression. Recently, it has found many applications to bioinformatics. In this paper, BWT is introduced from the view of combinatorics, and then an equivalence relation on words is proposed which shows that the transformation captures some common features of equivalent words. Based on the rationale that to what extent two words differ can be evaluated by the factors excluding their common features, a matrix representation for a DNA sequence is defined by means of a “subtraction operation” between the original word and its BWT word, thus a DNA sequences is converted into a 24-D vector whose components are the spectral norms of such matrices. To illustrate the use of the quantitative characterization of DNA sequences, phylogenetic trees of the full β-globin genes of 15 species and the S segments of 13 hantaviruses are constructed. The resulting monophyletic clusters agree well with the established taxonomic groups.
Abstract: Burrows-Wheeler Transform (BWT) is an extremely useful tool for textual lossless data compression. Recently, it has found many applications to bioinformatics. In this paper, BWT is introduced from the view of combinatorics, and then an equivalence relation on words is proposed which shows that the transformation captures some common features of equ...
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Analytic and Simulation Modeling of Plant-Animal Populations in Russian Tundra
Trashcheev Rostislav,
Boranbayev Askar,
Boranbayev Seilkhan,
Sarancha Dmitry,
Lyulyakin Oleg,
Yurezanskaya Yulia
Issue:
Volume 2, Issue 3, June 2014
Pages:
43-51
Received:
26 June 2014
Accepted:
8 July 2014
Published:
20 July 2014
Abstract: This article describes a mathematical modeling method of an ecological biology system; this method uses computers. Hypotheses about the leading mechanisms of fluctuations for tundra animals population’s number are formulated. An analysis of difference and differential equations and their manifestations in the community model “vegetation – lemmings – arctic foxes” and in an individual-oriented model of a lemming population are performed. This method uses research results including a full set of operations, namely from a substantiation of an object choice, a selection and processing of a biological information to the construction of a set of interconnected models. The given approach is used in the analysis of animal fluctuations by means of the tundra community models “vegetation – lemmings – arctic foxes”, “vegetation – reindeer”, and the individual-oriented model of the lemming population.
Abstract: This article describes a mathematical modeling method of an ecological biology system; this method uses computers. Hypotheses about the leading mechanisms of fluctuations for tundra animals population’s number are formulated. An analysis of difference and differential equations and their manifestations in the community model “vegetation – lemmings ...
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