A Novel Approach to Distinguish Between Intron-containing and Intronless Genes Based on the Format of Z Curves

Abstract

A novel method to distinguish between intron-containing and intronless DNA sequences has been proposed, based on different statistic behaviors between them. In this method, DNA sequences are first represented as Z curves. Three exponents α, β and γ for each given sequence are calculated based on the format of the Z curve for the DNA sequence. A three-dimensional space is spanned by the three exponents. Each DNA sequence may be represented by a point in this space. One hundred intronless and intron-containing genes, respectively, were selected randomly from the GenBank or EMBL database. It is shown that the 200 points are roughly distributed in different regions. The best separating plane to separate the two regions is obtained by using Fisher's discriminant algorithm. For any given sequence to be discriminated, calculate three exponents α, β and γ, corresponding to a point in the three-dimensional space. It the point is situated at the upper region of the separating plane, the sequence is discriminated as an intronless one; otherwise, the sequence is an intron-containing one. A test of the method for the sequences in an independent test set shows that the discriminant accuracy reaches as high as 89.0%.