Expansion and Integration of the IGS Annotation Engine

IGS注释引擎的扩展和集成

• 批准号: 8821628
• 负责人: Michelle Gwinn Giglio
• 金额: $ 30.7万
• 依托单位: UNIVERSITY OF MARYLAND BALTIMORE
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-09-15 至 2017-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8821628
• 关键词: Animals; Applications Grants; Area; Awareness; Bioconductor; Bioinformatics; Cloud Computing; Communicable Diseases; Communities; Complex; Computers; Data; Data Analyses; Data Set; Diagnostic; Disease Outbreaks; Drops; Drug Targeting; Education and Outreach; Environment; Evolution; Explosion; Faculty; Funding; Gene Expression Profile; Generations; Genome; Genotype; Goals; Health; Human; Imagery; Individual; Infectious Diseases Research; Informatics; Institutes; Internships; Link; National Institute of General Medical Sciences; Organism; Output; Pathway interactions; Plants; Process; Public Health; Qualifying; Research; Research Personnel; Research Project Grants; Resources; Running; Science; Scientist; Sequence Analysis; Services; Surveys; System; Technology; Training and Education; Ursidae Family; Work; acronyms; analytical method; artemis; cloud based; comparative genomics; computing resources; cost; disorder control; genome annotation; indexing; interest; interoperability; meetings; next generation; next generation sequencing; outreach; pathogen; response; statistics; tool; transcriptome sequencing; user-friendly; vaccine development; virtual

DESCRIPTION (provided by applicant): Recently, sequencing costs have dropped sharply due to increased throughput, simplification, and affordability of second (or even third and fourth) generation sequencing technologies, leading to an explosion of smaller sequencing facilities. However, despite the increased rate of sequence generation, there has not been a commensurate increase in access to computational resources to support high-quality sequence processing and analysis. The Annotation Engine has been effective in providing prokaryotic annotation services to the community for four years; however the analysis needs of researchers now far exceed prokaryotic genome annotation. In this work we plan to substantially expand the analysis pipelines offered in our service to include sequence assembly, comparative genomics, and transcriptome analysis. This will result in the evolution of the Annotation Engine into the Analysis Engine. Furthermore, we will also increase the interoperability of our tools with other popular bioinformatics tools. Finally, we will engage in active outreach and training. This combination of activities is expected to enable researchers to rapidly perform analyses that are vital for public health and have significant impact in the areas of drug targeting, diagnostic marker and genotyping, infectious disease control, rapid response to pathogen outbreaks and vaccine development.

描述（由申请人提供）：最近，由于第二次（甚至第三次和第四次）测序的通量、简化和可承受性的提高，测序成本急剧下降 世代测序技术，导致小型测序设施的爆炸式增长。然而，尽管序列生成速度有所提高，但支持高质量序列处理和分析的计算资源的获取却没有相应增加。注释引擎四年来一直有效地为社区提供原核注释服务；然而，现在研究人员的分析需求远远超出了原核基因组注释。在这项工作中，我们计划大幅扩展我们服务中提供的分析管道，包括序列组装、比较基因组学和转录组分析。这将导致注释引擎演变为分析引擎。此外，我们还将提高我们的工具与其他流行的生物信息学工具的互操作性。最后，我们将积极开展宣传和培训。这些活动的结合预计将使研究人员能够快速进行对公共卫生至关重要的分析，并在药物靶向、诊断标记和基因分型、传染病控制、对病原体爆发的快速反应和疫苗开发等领域产生重大影响。

项目成果

The IGS Standard Operating Procedure for Automated Prokaryotic Annotation.

• DOI: 10.4056/sigs.1223234
• 发表时间: 2011-04-29
• 期刊: Standards in genomic sciences
• 作者: Galens K;Orvis J;Daugherty S;Creasy HH;Angiuoli S;White O;Wortman J;Mahurkar A;Giglio MG
• 通讯作者: Giglio MG

Genomic Diversity in the Endosymbiotic Bacterium Rhizobium leguminosarum.

• DOI: 10.3390/genes9020060
• 发表时间: 2018-01-24
• 期刊: Genes
• 影响因子: 3.5
• 作者: Sánchez-Cañizares C;Jorrín B;Durán D;Nadendla S;Albareda M;Rubio-Sanz L;Lanza M;González-Guerrero M;Prieto RI;Brito B;Giglio MG;Rey L;Ruiz-Argüeso T;Palacios JM;Imperial J
• 通讯作者: Imperial J