Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center.
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center.
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DOI：
10.1093/nar/gkw1017
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发表时间：
2017-01-04
影响因子：
14.9
通讯作者：
Stevens RL
中科院分区：
文献类型：
--
作者：
Wattam AR;Davis JJ;Assaf R;Boisvert S;Brettin T;Bun C;Conrad N;Dietrich EM;Disz T;Gabbard JL;Gerdes S;Henry CS;Kenyon RW;Machi D;Mao C;Nordberg EK;Olsen GJ;Murphy-Olson DE;Olson R;Overbeek R;Parrello B;Pusch GD;Shukla M;Vonstein V;Warren A;Xia F;Yoo H;Stevens RL
病理系统资源整合中心(PATRIC)是细菌生物信息学资源中心(https://www.patricbrc.org).Patric最近的变化包括网络界面的重新设计和一些新的服务，这些服务为用户提供了一个平台，将他们从原始阅读带到综合分析体验。重新设计的界面允许研究人员直接访问工具和数据，重点已改为用户创建的基因组组，带有研究人员选择的数据的详细摘要和视图。也许最大的变化是研究人员分析他们的私人数据并将其与现有的公共数据进行比较的能力得到了增强。研究人员可以组装他们的原始序列读数，并使用RASTtk对重叠群进行注释。Patric还提供RNA-Seq、变异、模型重建和差异表达分析服务，所有这些都通过更新的私人工作空间提供。私人数据可以通过“虚拟整合”与帕特里克的任何公共数据进行比较。Patric中可供比较的基因组数量已扩大到8万多个，特别强调具有抗菌素耐药性数据的基因组。Patric使用这些数据来改进子系统注释和k-mer分类，并将新的基因组标记为具有指示对特定抗生素的敏感性或耐药性的签名。
The Pathosystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center (https://www.patricbrc.org). Recent changes to PATRIC include a redesign of the web interface and some new services that provide users with a platform that takes them from raw reads to an integrated analysis experience. The redesigned interface allows researchers direct access to tools and data, and the emphasis has changed to user-created genome-groups, with detailed summaries and views of the data that researchers have selected. Perhaps the biggest change has been the enhanced capability for researchers to analyze their private data and compare it to the available public data. Researchers can assemble their raw sequence reads and annotate the contigs using RASTtk. PATRIC also provides services for RNA-Seq, variation, model reconstruction and differential expression analysis, all delivered through an updated private workspace. Private data can be compared by ‘virtual integration’ to any of PATRIC's public data. The number of genomes available for comparison in PATRIC has expanded to over 80 000, with a special emphasis on genomes with antimicrobial resistance data. PATRIC uses this data to improve both subsystem annotation and k-mer classification, and tags new genomes as having signatures that indicate susceptibility or resistance to specific antibiotics.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
4.6
作者：
Davis JJ;Boisvert S;Brettin T;Kenyon RW;Mao C;Olson R;Overbeek R;Santerre J;Shukla M;Wattam AR;Will R;Xia F;Stevens R
通讯作者：
Stevens R
影响因子：
14.9
作者：
Clark K;Karsch-Mizrachi I;Lipman DJ;Ostell J;Sayers EW
通讯作者：
Sayers EW
影响因子：
14.9
作者：
Kodama Y;Shumway M;Leinonen R;International Nucleotide Sequence Database Collaboration
通讯作者：
International Nucleotide Sequence Database Collaboration
影响因子：
14.9
作者：
Frith MC;Wan R;Horton P
通讯作者：
Horton P