Gene teams with relaxed proximity constraint.

Proceedings. IEEE Computational Systems Bioinformatics Conference Pub Date : 2005-01-01 DOI:10.1109/csb.2005.33

Sun Kim, Jeong-Hyeon Choi, Jiong Yang

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引用次数: 28

Abstract

Functionally related genes co-evolve, probably due to the strong selection pressure in evolution. Thus we expect that they are present in multiple genomes. Physical proximity among genes, known as gene team, is a very useful concept to discover functionally related genes in multiple genomes. However, there are also many gene sets that do not preserve physical proximity. In this paper, we generalized the gene team model, that looks for gene clusters in a physically clustered form, to multiple genome cases with relaxed constraint. We propose a novel hybrid pattern model that combines the set and the sequential pattern models. Our model searches for gene clusters with and/or without physical proximity constraint. This model is implemented and tested with 97 genomes (120 replicons). The result was analyzed to show the usefulness of our model. Especially, analysis of gene clusters that belong to B. subtilis and E. coli demonstrated that our model predicted many experimentally verified operons and functionally related clusters. Our program is fast enough to provide a sevice on the web at http://platcom. informatics.indiana.edu/platcom/. Users can select any combination of 97 genomes to predict gene teams.

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具有宽松接近约束的基因团队。

功能相关的基因共同进化，可能是由于进化过程中强大的选择压力。因此，我们预计它们存在于多个基因组中。基因间的物理接近性，即基因团队，是发现多个基因组中功能相关基因的一个非常有用的概念。然而，也有许多基因组不能保持物理上的接近。本文将以物理聚类形式寻找基因簇的基因团队模型推广到具有宽松约束的多基因组案例中。提出了一种集模式和序列模式相结合的混合模式模型。我们的模型搜索有和/或没有物理接近约束的基因簇。该模型在97个基因组(120个复制子)上进行了实现和测试。对结果进行了分析，以表明我们模型的有效性。特别是，对枯草芽孢杆菌和大肠杆菌基因簇的分析表明，我们的模型预测了许多实验验证的操作子和功能相关簇。我们的程序足够快，可以在http://platcom网站上提供服务。informatics.indiana.edu/platcom/。用户可以选择97个基因组的任意组合来预测基因团队。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Proceedings. IEEE Computational Systems Bioinformatics Conference

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