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

Novák, Petr; Neumann, Pavel; Pech, Jiří; Steinhaisl, J.; Macas, Jiří

doi:https://dx.doi.org/10.1093/bioinformatics/btt054

Number of the records: 1

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

1.

SYSNO ASEP	0392350
Document Type	J - Journal Article
R&D Document Type	Journal Article
Subsidiary J	Článek ve WOS
Title	RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads
Author(s)	Novák, Petr (BC-A)_{RID, ORCID} Neumann, Pavel (BC-A)_{RID, ORCID} Pech, Jiří (BC-A) Steinhaisl, J. (CZ) Macas, Jiří (BC-A)_{RID, ORCID, SAI}
Source Title	Bioinformatics. - : Oxford University Press - ISSN 1367-4803 Roč. 29, č. 6 (2013), s. 792-793
Number of pages	2 s.
Publication form	Print - P
Language	eng - English
Country	GB - United Kingdom
Keywords	repetitiveDNA ; computational analysis ; next generation sequencing
Subject RIV	EB - Genetics ; Molecular Biology
R&D Projects	GBP501/12/G090 GA ČR - Czech Science Foundation (CSF)
	OC10037 GA MŠMT - Ministry of Education, Youth and Sports (MEYS)
Institutional support	BC-A - RVO:60077344
UT WOS	000316270400017
DOI	10.1093/bioinformatics/btt054
Annotation	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.
Workplace	Biology Centre (since 2006)
Contact	Dana Hypšová, eje@eje.cz, Tel.: 387 775 214
Year of Publishing	2014

Number of the records: 1