Collaborative Research: RUI: Interpolated Markov Models for DNA Sequence Analysis

这是马里兰州洛约拉学院的亚瑟德尔彻（RUI奖IIS-9820497）和基因组研究所的史蒂文萨尔茨伯格（奖IIS-9902923）的合作研究项目。DNA序列数据的数量正在爆炸式增长，并且随着这种增长，对用于序列分析的计算方法的需求也在平行增长。如此丰富的数据需要新的、高度精确的计算分析工具来探索这些序列，并最大限度地利用从中获得的科学知识。这个跨学科的项目将数据建模和数据挖掘的最新技术与分子生物学知识相结合，以在DNA序列数据库中找到基因和其他具有科学意义的模式。 Glimmer系统使用插值马尔可夫模型（IMM）来寻找微生物基因组中的基因。这个非常成功的系统已经发现了导致莱姆病，梅毒，结核病和其他疾病的细菌中超过98%的基因。该项目正在开发新的系统，以在更复杂的高等生物DNA中找到基因，同时推进IMM技术的最新发展。该项目的具体重点包括：开发用于基因发现的改进概率模型;开发用于识别横向转移基因和其他不寻常DNA序列的算法方法;以及开发用于分析高等生物（包括植物和哺乳动物）中DNA的IMM和其他概率技术。 该项目将极大地提高我们在各种生物体中发现基因和其他生物学重要特征的能力，从而开发新的抗生素和疫苗，并更好地了解DNA如何指导活细胞的功能。该软件将在基因组学网站community.http://www.tigr.org/softlab/glimmer/glimmer.html上免费传播。

This is a collaborative research project of Arthur Delcher at Loyola College at Maryland (RUI award IIS-9820497) and Steven Salzberg at the Institute for Genomic Research (award IIS-9902923). The quantity of DNA sequence data is exploding, and with this growth comes a parallel growth in the demand for computational methods for sequence analysis. This abundance of data demands new and highly accurate computational analysis tools to explore these sequences and maximize the scientific knowledge gained from them. This interdisciplinary project combines the latest techniques in data modeling and data mining with knowledge of molecular biology to find genes and other scientifically significant patterns in DNA sequence databases. The Glimmer system uses Interpolated Markov Models (IMMs) to finding genes in microbial genomes. This tremendously successful system has found over 98% of the genes in the bacteria that cause Lyme disease, syphilis, tuberculosis, and others. This project is developing new systems to find genes in the much more complex DNA of higher organisms, and at the same time advancing the state of the art for the underlying IMM technology. Specific foci of the project include: developing improved probabilistic models for gene finding; developing algorithmic methods for identifying laterally transferred genes and other unusual DNA sequences; and developing IMMs and other probabilistic techniques for analyzing DNA in higher organisms including plants and mammals. This project will dramatically improve our ability to discover genes and other biologically significant features in a wide range of organisms, leading to the development of new antibiotics and vaccines and to a better understanding of how DNA directs the functions of a living cell. The software will be freely disseminated in the genomics community.http://www.tigr.org/softlab/glimmer/glimmer.html