Browsing by Author "Bowman, Dale"

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Phylogenetic tree construction using trinucleotide usage profile (TUP)
(2016-10-06)
Chen, Si
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Deng, Lih-Yuan
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Bowman, Dale
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Shiau, Jyh-Jen Horng
;
Wong, Tit-Yee
Background: It has been a challenging task to build a genome-wide phylogenetic tree for a large group of species containing a large number of genes with long nucleotides sequences. The most popular method, called feature frequency profile (FFP-k), finds the frequency distribution for all words of certain length k over the whole genome sequence using (overlapping) windows of the same length. For a satisfactory result, the recommended word length (k) ranges from 6 to 15 and it may not be a multiple of 3 (codon length). The total number of possible words needed for FFP-k can range from 4(6) = 4096 to 4(15). Results: We propose a simple improvement over the popular FFP method using only a typical word length of 3. A new method, called Trinucleotide Usage Profile (TUP), is proposed based only on the (relative) frequency distribution using non-overlapping windows of length 3. The total number of possible words needed for TUP is 43 = 64, which is much less than the total count for the recommended optimal " resolution" for FFP. To build a phylogenetic tree, we propose first representing each of the species by a TUP vector and then using an appropriate distance measure between pairs of the TUP vectors for the tree construction. In particular, we propose summarizing a DNA sequence by a matrix of three rows corresponding to three reading frames, recording the frequency distribution of the non-overlapping words of length 3 in each of the reading frame. We also provide a numerical measure for comparing trees constructed with various methods. Conclusions: Compared to the FFP method, our empirical study showed that the proposed TUP method is more capable of building phylogenetic trees with a stronger biological support. We further provide some justifications on this from the information theory viewpoint. Unlike the FFP method, the TUP method takes the advantage that the starting of the first reading frame is (usually) known. Without this information, the FFP method could only rely on the frequency distribution of overlapping words, which is the average (or mixture) of the frequency distributions of three possible reading frames. Consequently, we show (from the entropy viewpoint) that the FFP procedure could dilute important gene information and therefore provides less accurate classification.
Secure and Fast Encryption (SAFE) with Classical Random Number Generators
(2018-08-01)
Deng, Lih-Yuan
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Shiau, Jyh-Jen Horng
;
Lu, Henry Horng-Shing
;
Bowman, Dale
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統計學研究所
Pseudo-random number generators (PRNGs) play an important role in both areas of computer simulation and computer security. Currently, there appears to be a huge divide between the types of PRNGs used in these two areas. For PRNGs in computer security applications, the security concern is extremely important. For PRNGs in computer simulation applications, the properties of high-dimensional equi-distribution, efficiency, long period-length, and portability are important. In recent years, there have been many PRNGs proposed in the area of computer simulation satisfying these nice properties. However, most of them are linear generators, thus sharing the same weakness in predictability. The major aim of this article is to propose a general class of secure generators, called SAFE (secure and fast encryption) generators, by properly "mixing" two baseline generators with the aforementioned properties to obtain a secure generator that would inherit these nice properties. Specifically, we propose applying a general mutual-shuffling method to certain linear generators, such as the currently most popular MT19937 generator and large-order multiple recursive generators, as well as outputting certain nonlinear transformations of the generated variates to construct secure PRNGS.