Computational Gene Modeling and Genome Sequence Assembly

描述(由申请人提供)： 该项目解决了两个主要的生物信息学问题：开发更好的软件来寻找真核生物基因组序列中的基因，以及为大型鸟枪式测序项目开发基因组组装器。基因发现项目将进行两个方面的工作：第一，我们将继续改进我们的广义隐马尔可夫模型和我们的一对隐马尔可夫模型基因发现者，随着新基因组的出现，培训他们适应新物种，并增强他们使用相关物种作为在新物种中发现基因的指南的能力。其次，我们将开发一种新的真核注释管道，该管道将整合来自广泛来源的结果，包括基因查找、蛋白质序列比对、cDNA和EST比对以及其他序列特征。这条管道将用于预测多个物种的综合基因集，特别是对现有注释不完整或过时的物种进行预测。这条管道还将作为一项服务，为其他群体注释基因组。汇编项目将包括几项主要工作。首先，我们将继续建立在我们成功的开源汇编程序项目AMOS的基础上，添加新的模块以实现与其他汇编程序包的互操作。其次，我们将开发新的组装器，可以处理焦磷酸测序数据、低覆盖率的基因组项目以及从复杂物种混合物中收集的序列。第三，我们将为基因组测序中心和其他合作者提供组装服务，帮助他们使用最新的组装工具组装基因组。这些将包括新的测序项目以及基因组，尽管已经测序，但可以使用改进的组装软件更准确地重新组装。对于所有的软件开发项目，我们将继续我们的做法，将我们的所有源代码免费提供给世界各地科学研究界的研究人员。

DESCRIPTION (provided by applicant): This project addresses two major bioinformatics problems: the development of better software for finding genes in eukaryotic genome sequences, and the development of genome assemblers for large shotgun sequencing projects. The gene finding project will pursue two tracks: first, we will continue to improve our Generalized Hidden Markov Model and our Pair Hidden Markov Model gene finders, training them for new species as new genomes appear, and enhancing their capabilities to use related species as a guide to gene finding in a new species. Second, we will develop a new eukaryotic annotation pipeline, which will integrate the results from a wide range of sources, including gene finders, protein sequence alignments, cDNA and EST alignments, and other sequence features. This pipeline will be used to predict comprehensive gene sets for multiple species, focusing especially on species for which the available annotation is incomplete or outdated. The pipeline will also be available as a service to annotate genomes for other groups. The assembler project will include several major efforts. First, we will continue to build on our successful open source assembler project, AMOS, adding new modules to allow inter-operation with other assembly packages. Second, we will develop new assemblers that can handle pyrosequencing data, low coverage genome projects, and sequences collected from complex mixtures of species. Third, we will provide assembly services to genome sequencing centers and other collaborators, helping them to assemble genomes using the latest available assembly tools. These will include new sequencing projects as well as genomes that, although already sequenced, can be re-assembled more accurately using improved assembly software. For all of the software development projects, we will continue our practice of making all our source code freely available to investigators in the scientific research community worldwide.