Similarity analysis of DNA sequences based on the weighted pseudo-entropy.
A DNA primary sequence is a string consisting of letters on an alphabet Ω = {a, c, g, t}. Based on all of the 2-combinations of the set Ω, here the repetition is allowed, we transform a DNA primary sequence into a special sequence over a set with cardinality 10. With the 10-letter sequence, we associate 10 nonnegative numerical sequences and then derive a 10-component vector by means of a weighted pseudo-entropy, which can reflect the information on elements of a sequence and, especially, the order relation among them. The new quantitative characterization of DNA sequences is sensitive to substitution of the string elements. The examination of the relationship among β-globin genes of 15 species illustrates the utility of the proposed approach.
Li
Chun
C
Department of Mathematics, Bohai University, Jinzhou 121013, People's Republic of China. lchlmb@yahoo.com.cn
Ma
Hong
H
Zhou
Yang
Y
Wang
Xiaolei
X
Zheng
Xiaoqi
X
D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D004247:DNA / Q000235:genetics*; D006801:Humans; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*; D055544:beta-Globins / Q000235:genetics
D055544:beta-Globins; D004247:DNA