Rephase Update-a Database of Repetitive Sequences

说明（由申请人提供）： Repbase Update（www.girinst.org）是一个重复元件数据库，目前代表了来自真核生物物种的3，200多个转座元件（TE）家族和亚家族。每个家族都有一个独特的名称，其注释包括生物学上有意义的信息，如物种起源，其系统分类，关键词，参考科学文献或贡献者的姓名，简短的评论等。或者在它们的共有序列和生物学分类方面已经被彻底修订。我们的方法是基于计算机辅助重建和分析公开的DNA序列数据。其他贡献来自同行评审的电子期刊Repbase Reports。RU已被世界各地的公共机构、基因组测序联盟和私营公司常规用于常规基因发现、多态性研究、序列组装和探针设计。RU内容已在原始同行评审的文章，评论和书籍章节中部分描述。该数据库成为具有生物学和医学重要性的个人研究项目以及创建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、索引并提供给研究人员。我们还将添加未确定数量的未注释的重复族。我们提出以下具体目标来迎接挑战： (1)继续检测、重建、注释和电子分发来自所有测序真核生物物种的重复家族的参考序列。(2)继续对重复家族进行系统分析和分类，并编写全面的词典，相互参照其命名和生物分类。(3)为RU的外部提交提供便利，并为不同研究小组编制的小型数据库提供协作支持。（四）、升级CENSOR程序，用于重复DNA的注释和分析，并继续生成选定基因组的重复元件图谱。(5)发展转座因子的自动化从头鉴定和分析。(6)组织小型研讨会，致力于重复命名法的培训和标准化。

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.