van Passel M W J, Luyf A C M, van Kampen A H C, Bart A, van der Ende A
Department of Medical Microbiology, Academic Medical Center 1100 DE Amsterdam, The Netherlands.
Bioinformatics. 2005 Jul 1;21(13):3053-5. doi: 10.1093/bioinformatics/bti460. Epub 2005 Apr 26.
Although whole-genome sequences have been analysed for the presence of anomalous DNA, no dedicated application is currently available to analyse the composition of individual sequence entries, for instance those derived by experimental techniques, such as subtractive hybridization. Since genomic dinucleotide frequency values are conserved between related species, a representative genome sequence can often be found to score for anomalous sequence composition for many of these putative horizontally transferred sequences. We developed the application deltarho-web, which enables the determination of the differences between the dinucleotide composition of an input sequence and that of a selected genome in a size-dependent manner. A feature allowing batch comparisons is included as well. In addition, deltarho-web allows the analysis of the dinucleotide composition of complete genomes. This provides complementary information for the identification of large anomalous gene clusters.
尽管已对全基因组序列进行分析以查找异常DNA的存在，但目前尚无专门用于分析单个序列条目的组成的应用程序，例如那些通过实验技术（如消减杂交）获得的序列。由于相关物种之间的基因组二核苷酸频率值是保守的，因此通常可以找到一个代表性的基因组序列，来对许多这些假定的水平转移序列的异常序列组成进行评分。我们开发了deltarho-web应用程序，它能够以大小依赖的方式确定输入序列与选定基因组的二核苷酸组成之间的差异。此外还包含一个允许批量比较的功能。此外，deltarho-web还允许分析完整基因组的二核苷酸组成。这为识别大型异常基因簇提供了补充信息。
