Kel A E, Kondrakhin Y V, Kel O V, Romashenko A G, Wingender E, Milanesi L, Kolchanov N A
Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia.
Proc Int Conf Intell Syst Mol Biol. 1995;3:197-205.
We present the computer tool FUNSITE for description and analysis of regulatory sequences of eukaryotic genomes. The tool consists of the following main parts: 1) An integrated database for genomic regulatory sequences. The integrated database was designed on the basis of the databases TRANSFAC (Wingender 1994) and TRRD (Kel et al. 1995) that are currently under development. The following functions are performed: i) linkage to the EMBL database; ii) preparing samples of definite types of functional sites with their flanking sequences; iii) preparing samples of promoter sequences; iv) preparing samples of transcription factors classified with regard to structural and functional features of DNA binding and activating domains, functional families of the factors, their tissue specificity and other functional features; v) access to data on mutual disposition of cis-elements within the regulatory regions. 2) The second component of FUNSITE tool is the set of programs for analysis of the structural organization of regulatory sequences: i) Program for revealing of potential transcription factors binding sites based on their consensi; ii) program for revealing of the potential binding sites using homology search with nucleotide sequences of real binding sites; iii) program for analysis of oligonucleotide context features which are characteristic of flank sequences of the binding sites; iv) program for design of recognition method for the functional sites based on generalized weight matrix; v) program for revealing potential composite elements. The results of analysis of the promoter sequences of eukaryotic genes with the FUNSITE are presented, too.
我们介绍了用于描述和分析真核生物基因组调控序列的计算机工具FUNSITE。该工具由以下主要部分组成：1）基因组调控序列的综合数据库。该综合数据库是在目前正在开发的TRANSFAC（Wingender，1994）和TRRD（Kel等人，1995）数据库的基础上设计的。其执行以下功能：i）与EMBL数据库的链接；ii）制备具有侧翼序列的特定类型功能位点的样本；iii）制备启动子序列的样本；iv）制备根据DNA结合和激活域的结构和功能特征、因子的功能家族、其组织特异性和其他功能特征分类的转录因子样本；v）获取调控区域内顺式元件相互位置的数据。2）FUNSITE工具的第二个组件是用于分析调控序列结构组织的程序集：i）基于共有序列揭示潜在转录因子结合位点的程序；ii）使用与真实结合位点的核苷酸序列进行同源性搜索来揭示潜在结合位点的程序；iii）分析结合位点侧翼序列特征性的寡核苷酸上下文特征的程序；iv）基于广义权重矩阵设计功能位点识别方法的程序；v）揭示潜在复合元件的程序。还展示了使用FUNSITE对真核基因启动子序列进行分析的结果。
