Phylogenetic tree construction using trinucleotide usage profile (TUP)

BMC Bioinformatics

Proceedings

Tit-Yee Wong¹  Lih-Yuan Deng²  Behrouz Madahian²  Dale Bowman²  Henry Horng-Shing Lu³  Jyh-Jen Horng Shiau³  Si Chen⁴ 

[1] Department of Biological Sciences, University of Memphis, Memphis, TN, USA;Department of Mathematical Sciences, University of Memphis, Memphis, TN, USA;Institute of Statistics, National Chiao Tung University, Hsinchu, Taiwan;Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and School of Pharmaceutical Sciences Wuhan University, Wuhan, China;

关键词: Feature frequency profile (FFP);    Reading frame;    Summary statistics;    Phylogenetic tree construction;    Tree comparison;   

DOI  :  10.1186/s12859-016-1222-3

来源: Springer

【 摘 要 】

BackgroundIt 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 46=4096 to 415.ResultsWe 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.ConclusionsCompared 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.

【 授权许可】

CC BY   
© The Author(s) 2016

【 图 表 】

Fig. 1

Fig. 12

Fig. 5

12936_2017_2014_Article_IEq61.gif

Fig. 3

Fig. 3

12936_2015_966_Article_IEq12.gif

Fig. 5

12936_2016_1315_Article_IEq9.gif

Fig. 3

Fig. 4

12944_2023_1932_Article_IEq4.gif

Fig. 1

Fig. 5

12944_2023_1932_Article_IEq1.gif

Fig. 3

Fig. 1