Repbase Update-a Database of Repetitive Sequences

描述(由申请人提供)： Repbase更新(http://www.girinst.org)是一个关系数据库，包含来自真核生物的8500多个转座元件家族和亚家族的重复元件。每个家族都可以通过一个唯一的名称来识别，其注释包括起源物种、系统分类、关键词、科学文献参考、投稿人姓名、简要评论等。在上一个周期中添加到Repbase更新(RU)的5198个重复家族中的大多数要么没有在其他地方报告，要么已经被彻底修订。我们的方法是基于公共DMA序列数据的计算机辅助重建和分析。原创稿件首先发表在一本名为《Repbase Reports》的电子期刊上。RU被世界各地的学术和研究机构用于基础研究和基因组注释。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需要以每年约1000个条目的速度增长，以满足基因组测序项目创造的需求。这些信息将被提取、重建、分析、注释、分类、索引，并通过互联网提供给研究人员。此外，我们还将发现和研究不同的超家族和保守重复序列，这是前沿研究的主要兴趣。我们提出以下具体目标： 迎接挑战：(1)继续检测、重建、注释和电子分配来自所有已测序真核物种的重复家族的参考序列(2)与测序联盟合作继续研究新测序的真核基因组中的TES(3)继续系统地鉴定和分析新的超家族和转座元件(TES)类别(4)挖掘和表征在真核基因组中保守的非编码区和顺式调控模块中过度表达的TES的残留物(5)组织两次会议，专门讨论与Repbase相关的研究、数据提交、数据传播、培训和重复命名的标准化。

DESCRIPTION (provided by applicant): Repbase Update (http://www.girinst.org) is a relational database of repetitive elements representing over 8500 families and subfamilies of transposable elements (TEs) from eukaryotes. Each family is identifiable by a unique name, and its annotation includes species of origin, systematic classification, keywords, reference to the scientific literature, names of contributors, brief commentaries, etc. Most of the 5198 repetitive families added to Repbase Update (RU) during the last cycle are either unreported anywhere else, or have been thoroughly revised. Our approach is based on computer-assisted reconstruction and analysis of public DMA sequence data. Original contributions are first reported in an electronic journal named Repbase Reports. RU is used throughout the world by academic and research institutions for basic research and genome annotations. 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 needs to grow at the rate of ~1000 entries per year to meet the demand created by the genome-sequencing projects. This information will be extracted, reconstructed, analyzed, annotated, classified, indexed and made available to researchers over the internet. In addition we will discover and study diverse superfamilies and conserved repeats, which are of primary interest for cutting-edge research. 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 studies of TEs in newly sequenced eukaryotic genomes in collaboration with sequencing consortia (3) continue systematic identification and analysis of new superfamilies and classes of transposable elements (TEs) (4) excavate and characterize remnants of TEs overrepresented in conserved non-coding regions and cis-regulatory modules in eukaryotic genomes (5) organize two conferences devoted to stimulation of Repbase-related research, data submission, data dissemination, training and standardization of repeat nomenclature.