基因组和染色体片段的序列和结构特征的可视化。在 CpG 岛、Alu 序列和整个基因组中的应用。

Visualization of sequence and structural features of genomes and chromosome fragments. Application to CpG islands, Alu sequences and whole genomes.

机构信息

Departament d'Enginyeria Quimica, Universitat Politècnica de Catalunya, Av. Diagonal 647, Barcelona, Spain.

出版信息

Gene. 2011 Mar 1;473(2):76-81. doi: 10.1016/j.gene.2010.11.008. Epub 2010 Dec 16.

DOI:10.1016/j.gene.2010.11.008

Abstract

A very simple new program is presented (G-SQUARES). It is useful in order to visualize the composition and basic structural features of whole genomes and selected chromosome regions. The frequency of all dimer and tetramer sequences is reported. Overall structural features are calculated, such as the tendency for alternation. A direct visual comparison among different sequences is easily available. Furthermore, the features which are visualized indicate further studies which should be carried out. Examples are presented on Alu sequences, CpG islands, whole eukaryotic and bacterial genomes.

摘要

现提出一个非常简单的新程序（G-SQUARES）。它可用于可视化整个基因组和选定染色体区域的组成和基本结构特征。报告了所有二聚体和四聚体序列的频率。计算了总体结构特征，例如交替倾向。不同序列之间的直接直观比较是容易实现的。此外，可视化的特征还指示应进行进一步的研究。以 Alu 序列、CpG 岛、整个真核生物和细菌基因组为例进行了说明。