Repbase Update, a database of repetitive elements in eukaryotic genomes

Repbase Update, a database of repetitive elements in eukaryotic genomes

2015 | Weidong Bao, Kenji K. Kojima, Oleksiy Kohany
Rebase Update (RU) is a well-curated database of transposable elements (TEs) and other repetitive sequences in eukaryotic genomes. Since its initial development in 1992, RU has been a fundamental resource for eukaryotic genome analysis and TE evolution studies. RU is maintained by the Genetic Information Research Institute (GIRI) and is accessible to academic and non-profit researchers upon registration. Commercial users require a license. RU and related libraries are downloaded approximately 500 times a month. Over the past three years, an average of 159 new users have been approved monthly. RU is accompanied by the e-journal "Repbase Reports" (RR), which acknowledges contributors and serves as a permanent record. RU contains over 38,000 sequences from more than 134 species, representing various TE families and subfamilies. These sequences include consensus sequences, which are used for TE classification and masking. RU also includes non-TE repeats such as satellite sequences and microsatellites, though these are not as thoroughly collected as in other databases. RU is used for TE identification and annotation, with tools like RECON and LTR_FINDER aiding in this process. TE classification is based on superfamily and clade definitions, with some classifications being phylogeny-based. RU entries are updated regularly, with new sequences added, existing sequences refined, and outdated entries removed. Users can submit sequences to RU or RR, with submissions requiring approval. The submission process involves a Java-based interface called RepbaseSubmitter. RU is essential for various tools and databases, including RepeatMasker and Dfam. RU is also used for genome analysis, with its data available in FASTA and EMBL formats. Future updates include an all-in-one file format and a reference protein library for each TE superfamily. RU continues to evolve to meet the needs of the research community while maintaining high-quality standards.Rebase Update (RU) is a well-curated database of transposable elements (TEs) and other repetitive sequences in eukaryotic genomes. Since its initial development in 1992, RU has been a fundamental resource for eukaryotic genome analysis and TE evolution studies. RU is maintained by the Genetic Information Research Institute (GIRI) and is accessible to academic and non-profit researchers upon registration. Commercial users require a license. RU and related libraries are downloaded approximately 500 times a month. Over the past three years, an average of 159 new users have been approved monthly. RU is accompanied by the e-journal "Repbase Reports" (RR), which acknowledges contributors and serves as a permanent record. RU contains over 38,000 sequences from more than 134 species, representing various TE families and subfamilies. These sequences include consensus sequences, which are used for TE classification and masking. RU also includes non-TE repeats such as satellite sequences and microsatellites, though these are not as thoroughly collected as in other databases. RU is used for TE identification and annotation, with tools like RECON and LTR_FINDER aiding in this process. TE classification is based on superfamily and clade definitions, with some classifications being phylogeny-based. RU entries are updated regularly, with new sequences added, existing sequences refined, and outdated entries removed. Users can submit sequences to RU or RR, with submissions requiring approval. The submission process involves a Java-based interface called RepbaseSubmitter. RU is essential for various tools and databases, including RepeatMasker and Dfam. RU is also used for genome analysis, with its data available in FASTA and EMBL formats. Future updates include an all-in-one file format and a reference protein library for each TE superfamily. RU continues to evolve to meet the needs of the research community while maintaining high-quality standards.
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