Počet záznamů: 1
RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads
- 1.
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, SAIZdroj.dok. Bioinformatics. - : Oxford University Press - ISSN 1367-4803
Roč. 29, č. 6 (2013), s. 792-793Poč.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