Loots Gabriela G, Ovcharenko Ivan
Genome Biology Division and EEBI Computing Division, Lawrence Livermore National Laboratory, 7000 East Avenue, L-441, Livermore, CA 94550, USA.
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W217-21. doi: 10.1093/nar/gkh383.
Identifying and characterizing the transcription factor binding site (TFBS) patterns of cis-regulatory elements represents a challenge, but holds promise to reveal the regulatory language the genome uses to dictate transcriptional dynamics. Several studies have demonstrated that regulatory modules are under positive selection and, therefore, are often conserved between related species. Using this evolutionary principle, we have created a comparative tool, rVISTA, for analyzing the regulatory potential of noncoding sequences. Our ability to experimentally identify functional noncoding sequences is extremely limited, therefore, rVISTA attempts to fill this great gap in genomic analysis by offering a powerful approach for eliminating TFBSs least likely to be biologically relevant. The rVISTA tool combines TFBS predictions, sequence comparisons and cluster analysis to identify noncoding DNA regions that are evolutionarily conserved and present in a specific configuration within genomic sequences. Here, we present the newly developed version 2.0 of the rVISTA tool, which can process alignments generated by both the zPicture and blastz alignment programs or use pre-computed pairwise alignments of several vertebrate genomes available from the ECR Browser and GALA database. The rVISTA web server is closely interconnected with the TRANSFAC database, allowing users to either search for matrices present in the TRANSFAC library collection or search for user-defined consensus sequences. The rVISTA tool is publicly available at http://rvista.dcode.org/.
识别并表征顺式调控元件的转录因子结合位点（TFBS）模式是一项挑战，但有望揭示基因组用于支配转录动态的调控语言。多项研究表明，调控模块处于正选择之下，因此在相关物种之间通常是保守的。利用这一进化原理，我们创建了一种比较工具rVISTA，用于分析非编码序列的调控潜力。我们通过实验识别功能性非编码序列的能力极其有限，因此，rVISTA试图通过提供一种强大的方法来消除最不可能具有生物学相关性的TFBS，从而填补基因组分析中的这一巨大空白。rVISTA工具结合了TFBS预测、序列比较和聚类分析，以识别在基因组序列中进化保守且以特定构型存在的非编码DNA区域。在此，我们展示了新开发的rVISTA工具2.0版本，它可以处理由zPicture和blastz比对程序生成的比对结果，或者使用从ECR浏览器和GALA数据库获取的几个脊椎动物基因组的预先计算的成对比对结果。rVISTA网络服务器与TRANSFAC数据库紧密相连，允许用户搜索TRANSFAC文库集合中存在的矩阵，或搜索用户定义的共有序列。rVISTA工具可在http://rvista.dcode.org/上公开获取。
