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Jurka, J. et al. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110, 462-467

Genetic Information Research Institute, Mountain View, CA 94043, USA.
Cytogenetic and Genome Research (Impact Factor: 1.91). 02/2005; 110(1-4):462-7. DOI: 10.1159/000084979
Source: PubMed

ABSTRACT Repbase Update is a comprehensive database of repetitive elements from diverse eukaryotic organisms. Currently, it contains over 3600 annotated sequences representing different families and subfamilies of repeats, many of which are unreported anywhere else. Each sequence is accompanied by a short description and references to the original contributors. Repbase Update includes Repbase Reports, an electronic journal publishing newly discovered transposable elements, and the Transposon Pub, a web-based browser of selected chromosomal maps of transposable elements. Sequences from Repbase Update are used to screen and annotate repetitive elements using programs such as Censor and RepeatMasker. Repbase Update is available on the worldwide web at http://www.girinst.org/Repbase_Update.html.

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    • "). Each cluster aligned was searched against Repbase (Jurka et al., 2005) using BLASTER (Quesneville et al., 2003) and HMMER (Johnson et al., 2010). A consensus feature was detected for each aligned cluster. "
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    • "The second pass also included the EST-and protein-based evidence as described in the first pass. All runs of MAKER included the masking of repetitive regions using REPEATMASKER v4.0.3 (Smit et al. 1996–2010) against the REPBASE v19.07 (Jurka et al. 2005) library. For each gene prediction, we selected the evidence with an annotation edit distance (AED) < 0.75. "
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