Počet záznamů: 1

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

SYSNO ASEP	0392350
Druh ASEP	J - Článek v odborném periodiku
Zařazení RIV	J - Článek v odborném periodiku
Poddruh J	Článek ve WOS
Název	RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads
Tvůrce(i)	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}
Zdroj.dok.	Bioinformatics. - : Oxford University Press - ISSN 1367-4803 Roč. 29, č. 6 (2013), s. 792-793
Poč.str.	2 s.
Forma vydání	Tištěná - P
Jazyk dok.	eng - angličtina
Země vyd.	GB - Velká Británie
Klíč. slova	repetitiveDNA ; computational analysis ; next generation sequencing
Vědní obor RIV	EB - Genetika a molekulární biologie
CEP	GBP501/12/G090 GA ČR - Grantová agentura ČR
	OC10037 GA MŠMT - Ministerstvo školství, mládeže a tělovýchovy
Institucionální podpora	BC-A - RVO:60077344
UT WOS	000316270400017
DOI	10.1093/bioinformatics/btt054
Anotace	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.
Pracoviště	Biologické centrum (od r. 2006)
Kontakt	Dana Hypšová, eje@eje.cz, Tel.: 387 775 214
Rok sběru	2014

Počet záznamů: 1