The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes
The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes
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DOI：
10.1186/1746-4811-5-8
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发表时间：
2009-06-19
期刊：
影响因子：
5.1
通讯作者：
Bennetzen, Jeffrey L.
中科院分区：
文献类型：
--
作者：
Estill, James C.;Bennetzen, Jeffrey L.
背景：复杂基因组中基因和转座元件的高质量注释需要人工整合多个计算证据来源。这些证据包括各种从头开始预测程序以及基于同源性的搜索的结果。大多数这些程序一次对单个连续序列进行操作，并且结果以多种可读格式生成，必须将这些格式转换为标准化文件格式。然后，这些翻译结果必须连接成单一来源，然后以集成形式呈现以供人工管理。结果：我们设计、实施和评估了一个名为 DAWGPAWS 的基于 Perl 的工作流程，用于生成计算结果，供人工管理植物基因组中的基因和转座元件。研究发现，使用 DAWGPAWS 可以将细菌人工染色体 (BAC) 载体中 80-200 kb 小麦 DNA 插入片段的注释速度提高约 20 倍，并且还可以显着提高注释质量的完整性和准确性。结论：DAWGPAWS 基因组注释管道通过在植物基因组注释中生成计算证据，满足了植物基因组注释的重要需求。 以高吞吐量的方式将这些结果转换为通用文件格式，并促进对这些计算结果的人工管理。我们通过使用此管道注释来自六倍体小麦基因组 (Triticum aestivum L.) 的 220 个 BAC 插入中的基因和转座元件，验证了 DAWGPAWS 的价值。 DAWGPAWS 可以应用于其他植物基因组的注释工作，只需对特定于程序的配置文件进行少量修改，并且工作流程的模块化设计有助于集成到现有管道中。
Background: High quality annotation of the genes and transposable elements in complex genomes requires a human-curated integration of multiple sources of computational evidence. These evidences include results from a diversity of ab initio prediction programs as well as homology-based searches. Most of these programs operate on a single contiguous sequence at a time, and the results are generated in a diverse array of readable formats that must be translated to a standardized file format. These translated results must then be concatenated into a single source, and then presented in an integrated form for human curation.Results: We have designed, implemented, and assessed a Perl-based workflow named DAWGPAWS for the generation of computational results for human curation of the genes and transposable elements in plant genomes. The use of DAWGPAWS was found to accelerate annotation of 80-200 kb wheat DNA inserts in bacterial artificial chromosome (BAC) vectors by approximately twenty-fold and to also significantly improve the quality of the annotation in terms of completeness and accuracy.Conclusion: The DAWGPAWS genome annotation pipeline fills an important need in the annotation of plant genomes by generating computational evidences in a high throughput manner, translating these results to a common file format, and facilitating the human curation of these computational results. We have verified the value of DAWGPAWS by using this pipeline to annotate the genes and transposable elements in 220 BAC insertions from the hexaploid wheat genome (Triticum aestivum L.). DAWGPAWS can be applied to annotation efforts in other plant genomes with minor modifications of program-specific configuration files, and the modular design of the workflow facilitates integration into existing pipelines.