RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads

0392350 - BC 2014 RIV GB eng J - Journal Article
Novák, Petr - Neumann, Pavel - Pech, Jiří - Steinhaisl, J. - Macas, Jiří
RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads.
Bioinformatics. Roč. 29, č. 6 (2013), s. 792-793. ISSN 1367-4803. E-ISSN 1460-2059
R&D Projects: GA ČR GBP501/12/G090; GA MŠMT(CZ) OC10037
Institutional support: RVO:60077344
Keywords : repetitiveDNA * computational analysis * next generation sequencing
Subject RIV: EB - Genetics ; Molecular Biology
Impact factor: 4.621, year: 2013

Motivation: Repetitive DNA makes up large portions of plant and animal nuclear genomes, yet it remains the least-characterized genome component in most species studied so far. Although the recent availability of high-throughput sequencing data provides necessary resources for in-depth investigation of genomic repeats, its utility is hampered by the lack of specialized bioinformatics tools and appropriate computational resources that would enable large-scale repeat analysis to be run by biologically oriented researchers. Results: Here we present RepeatExplorer, a collection of software tools for characterization of repetitive elements, which is accessible via web interface. A key component of the server is the computational pipeline using a graph-based sequence clustering algorithm to facilitate de novo repeat identification without the need for reference databases of known elements. Because the algorithm uses short sequences randomly sampled from the genome as input, it is ideal for analyzing next-generation sequence reads.
Permanent Link: http://hdl.handle.net/11104/0221235