ESTIMA, a tool for EST management in a multi-project environment.
ESTIMA, a tool for EST management in a multi-project environment.
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DOI：
10.1186/1471-2105-5-176
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发表时间：
2004-11-04
影响因子：
3
通讯作者：
Liu L
中科院分区：
文献类型：
--
作者：
Kumar CG;LeDuc R;Gong G;Roinishivili L;Lewin HA;Liu L
互补 DNA (cDNA) 文库的单次部分测序可生成数千个色谱图，这些色谱图被处理成高质量的表达序列标签 (EST)，然后组装成代表推定基因的重叠群。通常，为了有价值，EST 和重叠群必须与有意义的注释相关联，并可供最终用户使用。为了满足多个高通量 EST 测序项目的 EST 注释和数据管理要求，我们创建了一个 Web 应用程序“表达序列标签信息管理和注释”(ESTIMA)。它以单个 EST 为基础，并围绕 EST 的不同属性进行组织，包括色谱图、碱基识别质量评分、组装转录本的结构以及用于推断功能注释、基因本体关联和 cDNA 库信息的多个比较源。 ESTIMA 由一个关系数据库模式和一组交互式查询接口组成。它们与一套基于网络的工具集成在一起，允许用户查询和检索信息。此外，查询结果在各种 EST 属性之间相互关联。 ESTIMA 有几个独特的功能。用户可以运行自己的 EST 处理流程，搜索首选参考基因组，并使用任何聚类和组装算法。 ESTIMA 数据库模式非常灵活，可以接受任何 EST 处理和组装管道的输出。 ESTIMA 已用于许多物种的 EST 项目管理，包括蜜蜂 (Apis mellifera)、牛 (Bos taurus)、鸣禽 (Taeniopygia guttata)、玉米根虫 (Diabrotica vergifera)、鲶鱼 (Ictalurus punctatus、Ictalurusfurcatus) 和苹果 (Malus x Domestica)。整个资源可以按原样下载和使用，也可以轻松修改以满足其他 cDNA 测序项目的独特需求。用于创建 ESTIMA 界面的脚本可以以存档格式免费提供给学术用户。实体关系 (E-R) 图和用于生成 Oracle 数据库表的程序也可用。我们还在同一网站上提供了详细的安装说明和教程。目前，色谱图、EST 数据库及其注释已可用于牛和蜜蜂大脑 EST 项目。非学术用户需要联系 W.M.伊利诺伊大学厄巴纳-香槟分校凯克功能和比较基因组学中心，伊利诺伊州厄巴纳市，获取许可信息。
Single-pass, partial sequencing of complementary DNA (cDNA) libraries generates thousands of chromatograms that are processed into high quality expressed sequence tags (ESTs), and then assembled into contigs representative of putative genes. Usually, to be of value, ESTs and contigs must be associated with meaningful annotations, and made available to end-users. A web application, Expressed Sequence Tag Information Management and Annotation (ESTIMA), has been created to meet the EST annotation and data management requirements of multiple high-throughput EST sequencing projects. It is anchored on individual ESTs and organized around different properties of ESTs including chromatograms, base-calling quality scores, structure of assembled transcripts, and multiple sources of comparison to infer functional annotation, Gene Ontology associations, and cDNA library information. ESTIMA consists of a relational database schema and a set of interactive query interfaces. These are integrated with a suite of web-based tools that allow a user to query and retrieve information. Further, query results are interconnected among the various EST properties. ESTIMA has several unique features. Users may run their own EST processing pipeline, search against preferred reference genomes, and use any clustering and assembly algorithm. The ESTIMA database schema is very flexible and accepts output from any EST processing and assembly pipeline. ESTIMA has been used for the management of EST projects of many species, including honeybee (Apis mellifera), cattle (Bos taurus), songbird (Taeniopygia guttata), corn rootworm (Diabrotica vergifera), catfish (Ictalurus punctatus, Ictalurus furcatus), and apple (Malus x domestica). The entire resource may be downloaded and used as is, or readily adapted to fit the unique needs of other cDNA sequencing projects. The scripts used to create the ESTIMA interface are freely available to academic users in an archived format from . The entity-relationship (E-R) diagrams and the programs used to generate the Oracle database tables are also available. We have also provided detailed installation instructions and a tutorial at the same website. Presently the chromatograms, EST databases and their annotations have been made available for cattle and honeybee brain EST projects. Non-academic users need to contact the W.M. Keck Center for Functional and Comparative Genomics, University of Illinois at Urbana-Champaign, Urbana, IL, for licensing information.