Repbase Update (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.
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