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

Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. Research Abstract Details 

Research Abstract Table of Contents

Jump to the:

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

Oleksiy Kohany,Andrew J Gentles,Lukasz Hankus,Jerzy Jurka,

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 (RepbaseSubmitter) and http://www.girinst.org/censor/index.php (Censor).

Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. Publishing Authors By Initials

O Kohany,AJ Gentles,L Hankus,J Jurka,

For similar information science: computing methodologies: software research abstracts see: information science: computing methodologies: software research

PUBMED ID PMID:

MEDLINE DATE:

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

PUBLICATION TYPE: Research Support, N.I.H., Extr

Journal: BMC bioinformatics

VOLUME: 7

Page Numbers: 474

Journal Abbreviation: BMC Bioinformatics

ISSN: 1471-2105

DAY: 25

MONTH: 10

YEAR: 2006

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

Number of References:

LANGUAGE: eng

NlmUniqueID: 100965194

Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. Keywords Mesh Terms:

KEYWORDS: Software

MESH TERMS: genetics

Chemical & Substance for Abstract: Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. Information

Substance Name: Retroelements

Registry Number: 0

Grant and Affiliation Information for Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor.

AFFILIATION: Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043, USA. kohany@girinst.org

Country: England

AGENCY: United States NLM

GRANT: 5 P41 LM006252-08

ACRONYM: LM

MEDLINETA: BMC Bioinformatics

REFSOURCE:

DATABASENAME:

ACCESSION NUMBER:

Number Hits: 0

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

• A universal classification of eukaryotic transposable elements implemented in Repbase.
• Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor.
• Conserved eukaryotic transposable elements and the evolution of gene regulation.
• Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica.
• Helitrons on a roll: eukaryotic rolling-circle transposons.
• Repetitive sequences in complex genomes: structure and evolution.
• VisualRepbase: an interface for the study of occurrences of transposable element families.