Galaxy tools to study genome diversity
Galaxy tools to study genome diversity
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DOI：
10.1186/2047-217x-2-17
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发表时间：
2013-01-01
期刊：
影响因子：
9.2
通讯作者：
Miller, Webb
中科院分区：
文献类型：
--
作者：
Bedoya-Reina, Oscar C.;Ratan, Aakrosh;Miller, Webb
背景：种内遗传变异可用于研究非模型脊椎动物的种群结构、选择和基因流；由于基因组测序成本大幅下降，小型实验室现在可以从感兴趣的物种中获取全基因组变异数据。然而，这些实验室可能不容易访问和熟悉用于分析这些数据的计算工具。结果：我们为 Galaxy 网络服务器创建了一套工具，旨在处理通过对同一物种的多个个体进行全基因组测序或使用 SNP 基因分型微阵列发现的核苷酸和氨基酸多态性。除了提供用户友好的工具外，主要目标是使已发表的分析具有可重复性。虽然本文讨论的大多数示例都涉及非人类脊椎动物的核基因组多样性，但我们还说明了这些工具在真菌基因组、人类生物医学数据和线粒体序列中的应用。 结论：该项目说明一个小组可以设计、实施、测试、记录和分发 Galaxy 工具集合，以满足特定生物学家群体的需求。
Background: Intra-species genetic variation can be used to investigate population structure, selection, and gene flow in non-model vertebrates; and due to the plummeting costs for genome sequencing, it is now possible for small labs to obtain full-genome variation data from their species of interest. However, those labs may not have easy access to, and familiarity with, computational tools to analyze those data.Results: We have created a suite of tools for the Galaxy web server aimed at handling nucleotide and amino-acid polymorphisms discovered by full-genome sequencing of several individuals of the same species, or using a SNP genotyping microarray. In addition to providing user-friendly tools, a main goal is to make published analyses reproducible. While most of the examples discussed in this paper deal with nuclear-genome diversity in non-human vertebrates, we also illustrate the application of the tools to fungal genomes, human biomedical data, and mitochondrial sequences.Conclusions: This project illustrates that a small group can design, implement, test, document, and distribute a Galaxy tool collection to meet the needs of a particular community of biologists.