Rephase Update-a Database of Repetitive Sequences

0描述(由申请人提供)： Repbase更新(http://www.girinst.org)是一个重复元件的数据库，目前代表来自真核物种的3,200多个转座元件(TES)家族和亚家族。每个家族都可以通过一个唯一的名称来识别，其注释包括生物学上有意义的信息，如起源物种、其系统分类、关键词、对科学文献的参考或撰稿人的姓名、简要评论等。在上一个周期中添加到Repbase更新(RU)的1,799个重复家族中的大多数要么在其他地方没有报道，要么在其共识序列和生物分类方面得到了彻底的修订。我们的方法是基于计算机辅助重建和分析公开可用的DNA序列数据。其他投稿来自同行评议的电子期刊《Repbase Reports》。RU经常被世界各地的公共机构、基因组测序联盟和私人公司用于常规的基因发现、多态研究、序列组装和探针设计。RU的内容在最初的同行评议文章、评论和书籍章节中进行了部分描述。该数据库成为具有生物学和医学重要性的个别研究项目和建立二级数据库的独特资源。 在接下来的五年里，RU的规模预计将翻一番。这些信息将被提取、重建、分析、注释、分类、编入索引并提供给研究人员。我们还将添加数量未确定的未注释重复族。为迎接这一挑战，我们提出了以下具体目标： (1)继续检测、重建、注释和电子分布所有已测序的真核生物中重复家族的参考序列。(2)继续对重复家系进行系统分析和分类，并编制综合词典，交叉参考其命名和生物学分类。(3)促进外部向研究组提交意见，并为不同研究小组编制的较小数据库提供协作支持。(4)。升级重复DNA注释和分析的审查程序，并继续为选定的基因组生成重复元素图。(5)发展转座元件的自动从头识别和分析。(6)组织小型讲习班，专门对重复命名法进行培训和标准化。

0DESCRIPTION (provided by applicant): Repbase Update (http://www.girinst.org) is a database of repetitive elements currently representing over 3,200 families and subfamilies of transposable elements (TEs) from eukaryotic species. Each family is identifiable by a unique name, and its annotation includes biologically meaningful information such as species of origin, its systematic classification, keywords, reference to the scientific literature or names of contributors, brief commentaries, etc. Most of the 1,799 repetitive families added to Repbase Update (RU) during the last cycle are either unreported anywhere else, or have been thoroughly revised in terms of their consensus sequences and biological classification. Our approach is based on computer-assisted reconstruction and analysis of publicly available DNA sequence data. Additional contributions come via the peer-reviewed electronic journal Repbase Reports. RU has been routinely used by public institutions, genome sequencing consortia, and private companies throughout the world in routine gene discovery, polymorphism studies, sequence assembly and probe design. RU content has been partially described in original peer-reviewed articles, reviews and book chapters. This database became a unique resource for individual research projects of biological and medical importance and for creation of secondary databases. During the next five years RU is expected to double its size. This information will be extracted, reconstructed, analyzed, annotated, classified, indexed and made available to researchers. We will also add an undetermined number of unannotated repetitive families. We propose the following specific aims to meet the challenge: (1) Continue detection, reconstruction, annotation and electronic distribution of reference sequences for repetitive families from all sequenced eukaryotic species. (2) Continue systematic analysis and classification of repetitive families and prepare comprehensive dictionaries cross-referencing their nomenclature and biological classification. (3) Facilitate external submissions to RU and provide collaborative support to smaller databases compiled by different research groups. (4). Upgrade CENSOR program for annotation and analysis of repetitive DNA and continue generating maps of repetitive elements for selected genomes. (5) Pursue development of automated de novo identification and analysis of transposable elements. (6) Organize small workshops devoted to training and standardization of repeat nomenclature.