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Open Access Software

Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor

Oleksiy Kohany1, Andrew J Gentles2, Lukasz Hankus1 and Jerzy Jurka1*

Author Affiliations

1 Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043, USA

2 School of Medicine, Stanford University Stanford, CA 94301, USA

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BMC Bioinformatics 2006, 7:474  doi:10.1186/1471-2105-7-474

Published: 25 October 2006

Abstract

Background

Repbase is a reference database of eukaryotic repetitive DNA, which includes prototypic sequences of repeats and basic information described in annotations. Updating and maintenance of the database requires specialized tools, which we have created and made available for use with Repbase, and which may be useful as a template for other curated databases.

Results

We describe the software tools RepbaseSubmitter and Censor, which are designed to facilitate updating and screening the content of Repbase. RepbaseSubmitter is a java-based interface for formatting and annotating Repbase entries. It eliminates many common formatting errors, and automates actions such as calculation of sequence lengths and composition, thus facilitating curation of Repbase sequences. In addition, it has several features for predicting protein coding regions in sequences; searching and including Pubmed references in Repbase entries; and searching the NCBI taxonomy database for correct inclusion of species information and taxonomic position. Censor is a tool to rapidly identify repetitive elements by comparison to known repeats. It uses WU-BLAST for speed and sensitivity, and can conduct DNA-DNA, DNA-protein, or translated DNA-translated DNA searches of genomic sequence. Defragmented output includes a map of repeats present in the query sequence, with the options to report masked query sequence(s), repeat sequences found in the query, and alignments.

Conclusion

Censor and RepbaseSubmitter are available as both web-based services and downloadable versions. They can be found at http://www.girinst.org/repbase/submission.html webcite (RepbaseSubmitter) and http://www.girinst.org/censor/index.php webcite (Censor).