title: RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads.
abstract: BACKGROUND
  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. Additional tools are provided to aid in classification of identified repeats, investigate phylogenetic relationships of retroelements and perform comparative analysis of repeat composition between multiple species. The server allows to analyze several million sequence reads, which typically results in identification of most high and medium copy repeats in higher plant genomes.
authors: Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic.
authors: Petr
authors: P
authors: Novák
authors: Pavel
authors: P
authors: Neumann
authors: Jiří
authors: J
authors: Pech
authors: Jaroslav
authors: J
authors: Steinhaisl
authors: Jiří
authors: J
authors: Macas
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D004247:DNA / Q000737:chemistry*; D056890:Eukaryota / Q000235:genetics; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D020407:Internet; D010802:Phylogeny; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D004247:DNA