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

By Oleksiy Kohany, Andrew J. Gentles, Lukasz Hankus, Jerzy Jurka. BMC Bioinformatics, 2006

873 citations recorded by the source corpus.

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

Subfields: Ecology, Evolution, Behavior and Systematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e48c911667636003ca6d2bca32f87557661dc157

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In Molecular Biology

Citations in the corpus

The Dfam database of repetitive DNA families (2015, background): “(1–3)), followed by homology-based annotation (4), in which tools are used to seek all recognizable members of those families.”
Repbase Update, a database of repetitive elements in eukaryotic genomes (2015, methodology): “The primary consideration for inclusion in RU is the novelty of the sequence, which can be checked conveniently at our Censor service (http://girinst.org/ censor/index.php) [8].”
Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics (2013, methodology): “In order to remove transposon-related genes from the annotation data set, we masked repetitive sequences in the transcript sequences using CENSOR (Kohany et al. 2006) with the MIPS Repeat Element Database (Spannagl et al. 2007) and the Plant Repeat Databases version 3 of Michigan State University…”