VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data.
VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data.
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DOI：
10.1186/1471-2164-13-131
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发表时间：
2012-04-05
期刊：
影响因子：
4.4
通讯作者：
Webb-Robertson BJ
中科院分区：
文献类型：
--
作者：
Peterson ES;McCue LA;Schrimpe-Rutledge AC;Jensen JL;Walker H;Kobold MA;Webb SR;Payne SH;Ansong C;Adkins JN;Cannon WR;Webb-Robertson BJ
基因组测序和组装的程序方面已经变得相对便宜，但这些基因组的完整，准确的结构注释仍然是一个挑战。下一代测序转录组学（RNA-Seq），全球微阵列和基于串联质谱（MS/MS）的蛋白质组学已经证明了基因组管理者作为个人信息来源的巨大价值，然而，整合这些数据类型以验证和改进结构注释仍然是一个重大挑战。目前的可视化和统计分析工具集中在单一的数据类型上，或者对现有的软件工具进行改造以分析新的数据形式。我们提出的可视化探索和统计促进注释（VESPA）是一个新的交互式可视化分析软件工具，专注于帮助科学家与注释的原核基因组，通过整合蛋白质组学和转录组学数据与当前的基因组位置坐标。VESPA是一个桌面Java™应用程序，它将高通量蛋白质组学数据（以肽为中心）和转录组学（探针或RNA-Seq）数据集成到基因组环境中，所有这些数据都可以在三个基因组分辨率水平上可视化。通过与基因组可视化相关联的搜索来查询数据，以找到具有高错误注释可能性的区域。检索结果与导出结果相关联，以便在VESPA之外进行进一步验证，或者通过与BLAST的相互作用，可以与软件同时分析潜在的编码区。VESPA在两个用例（鼠疫耶尔森氏菌F和聚球藻PCC 7002）上进行了演示，以证明可以使用单独的蛋白质组学数据或与转录组学数据相结合的快速方式在VESPA中发现和探索错误注释。VESPA是一种交互式可视化分析工具，它将高通量数据整合到基因组背景中，以促进原核基因组中结构错误注释的发现。通过多层次的基因组分辨率、关联搜索和与现有生物信息学工具的交互进行可视化分析，对数据进行评估。我们强调了VESPA的新颖功能以及为客户端应用程序可视化这些大型异构数据集的核心编程要求。该软件可在https://www.biopilot.org/docs/Software/Vespa.php上免费获得。
The procedural aspects of genome sequencing and assembly have become relatively inexpensive, yet the full, accurate structural annotation of these genomes remains a challenge. Next-generation sequencing transcriptomics (RNA-Seq), global microarrays, and tandem mass spectrometry (MS/MS)-based proteomics have demonstrated immense value to genome curators as individual sources of information, however, integrating these data types to validate and improve structural annotation remains a major challenge. Current visual and statistical analytic tools are focused on a single data type, or existing software tools are retrofitted to analyze new data forms. We present Visual Exploration and Statistics to Promote Annotation (VESPA) is a new interactive visual analysis software tool focused on assisting scientists with the annotation of prokaryotic genomes though the integration of proteomics and transcriptomics data with current genome location coordinates. VESPA is a desktop Java™ application that integrates high-throughput proteomics data (peptide-centric) and transcriptomics (probe or RNA-Seq) data into a genomic context, all of which can be visualized at three levels of genomic resolution. Data is interrogated via searches linked to the genome visualizations to find regions with high likelihood of mis-annotation. Search results are linked to exports for further validation outside of VESPA or potential coding-regions can be analyzed concurrently with the software through interaction with BLAST. VESPA is demonstrated on two use cases (Yersinia pestis Pestoides F and Synechococcus sp. PCC 7002) to demonstrate the rapid manner in which mis-annotations can be found and explored in VESPA using either proteomics data alone, or in combination with transcriptomic data. VESPA is an interactive visual analytics tool that integrates high-throughput data into a genomic context to facilitate the discovery of structural mis-annotations in prokaryotic genomes. Data is evaluated via visual analysis across multiple levels of genomic resolution, linked searches and interaction with existing bioinformatics tools. We highlight the novel functionality of VESPA and core programming requirements for visualization of these large heterogeneous datasets for a client-side application. The software is freely available at https://www.biopilot.org/docs/Software/Vespa.php.
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影响因子：
3.4
作者：
Deutsch, Eric W.;Mendoza, Luis;Shteynberg, David;Farrah, Terry;Lam, Henry;Tasman, Natalie;Sun, Zhi;Nilsson, Erik;Pratt, Brian;Prazen, Bryan;Eng, Jimmy K.;Martin, Daniel B.;Nesvizhskii, Alexey I.;Aebersold, Ruedi
通讯作者：
Aebersold, Ruedi
影响因子：
5.8
作者：
Polpitiya, Ashoka D.;Qian, Wei-Jun;Smith, Richard D.
通讯作者：
Smith, Richard D.
影响因子：
7
作者：
Skinner, Mitchell E.;Uzilov, Andrew V.;Holmes, Ian H.
通讯作者：
Holmes, Ian H.
影响因子：
3.3
作者：
Castellana N;Bafna V
通讯作者：
Bafna V
GBROWSE MOBY：基于网络的生物摩托服务浏览器。
影响因子：
--
作者：
Wilkinson, Mark
通讯作者：
Wilkinson, Mark