A Novel Method to Calculate the G+C Content of Genomic DNA Sequences

Abstract

The base composition of a DNA fragment or genome is usually measured by the proportion of A+T or G+C in the sequence. The G+C content along genomic sequences is usually calculated using an overlapping or non-overlapping sliding window method. The result and accuracy of such an approach depends on the size of the window and the moving distance adopted. In this paper, a novel windowless technique to calculate the G+C content of genomic sequences is proposed. By this method, the G+C content can be calculated at different "resolution". In an extreme case, the G+C content may be computed at a specific point, rather than in a window of finite size. This is particularly useful to analyze the fine variation of base composition along genomic sequences. As the first example, the variation of G+C content along each of 16 yeast chromosomes is analyzed. The G+C-rich regions with length larger than 5 kb sequences are detected and listed in details. It is found that each chromosome consists of several G+C-rich and G+C-poor regions alternatively, i.e., a mosaic structure. Another example is to analyze the G+C content for each of the two chromosomes of the Vibrio cholerae genome. Based on the variations of the G+C content in each chromosome, it is shown that some fragments in the Vibrio cholerae genome may have been transferred from other species. Especially, the position and size of the large integron island on the smaller chromosome was precisely predicted. This method would be a useful tool for analyzing genomic sequences.

Statistical analyses of conserved features of genomic islands in bacteria

“…The homogeneity feature was obtained based on the cumulative GC profile (Zhang et al, 2001). The method of the cumulative GC profile proposed by Zhang and colleagues has been used to identify GIs in dozens of prokaryotic genomes (Charkowski, 2004;Greub et al, 2004;Chen, 2006;Do and Miyano, 2008;Zhang and Zhang, 2004a,b, 2005Wei and Guo, 2011).…”

Identification of genomic islands in six plant pathogens

“…Based on z n , the GC content can be calculated using a windowless technique (Zhang et al, 2001). Usually, for an ATrich genome, z n is approximately a monotonously increasing linear function of n, whereas for a GC-rich genome, z n is approximately a monotonously decreasing linear function of n. In both cases, it is convenient to fit the curve of z n ∼n by a straight line using the least square technique,…”

“…Recently, a windowless method for calculating the GC content has been proposed, which has a higher resolution in detecting the change of genomic GC content compared to the traditional window-based method (Zhang et al, 2001). Based on the cumulative GC profile, GIs in the genomes of Corynebacterium glutamicum, Vibrio vulnificus (Zhang and Zhang, 2004b) and Rhodopseudomonas palustris (Zhang and Zhang, 2004a) have been identified.…”

Genomic Islands in the Corynebacterium efficiens Genome

“…The region ⌬n is usually chosen to be a fragment of a natural DNA sequence, e.g., a genomic island. Equation 4 describes the windowless technique for the GC content computation (12). An index to measure codon usage bias.…”

“…The window-based method has a low resolution in detecting the GC content change. We recently proposed a windowless method for the GC content computation, the cumulative GC profile, which is much more sensitive to detecting GC content change than the traditional window-based method (12,14,15). In the present study, we used the cumulative GC profile to identify genomic islands in the C. efficiens genome.…”