Počet záznamů: 1

Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data

SYSNO ASEP	0347465
Druh ASEP	J - Článek v odborném periodiku
Zařazení RIV	J - Článek v odborném periodiku
Poddruh J	Článek ve WOS
Název	Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data
Tvůrce(i)	Novák, Petr (BC-A)_{RID, ORCID} Neumann, Pavel (BC-A)_{RID, ORCID} Macas, Jiří (BC-A)_{RID, ORCID, SAI}
Celkový počet autorů	3
Zdroj.dok.	BMC Bioinformatics. - : BioMed Central - ISSN 1471-2105 Roč. 11, č. 1 (2010), s. 378-389
Poč.str.	12 s.
Jazyk dok.	eng - angličtina
Země vyd.	GB - Velká Británie
Klíč. slova	repetitive DNA ; plant genome ; next generation sequencing
Vědní obor RIV	EB - Genetika a molekulární biologie
CEP	OC10037 GA MŠMT - Ministerstvo školství, mládeže a tělovýchovy
	LC06004 GA MŠMT - Ministerstvo školství, mládeže a tělovýchovy
CEZ	AV0Z50510513 - UMBR-M, BC-A (2005-2011)
UT WOS	000281440900001
DOI	10.1186/1471-2105-11-378
Anotace	We adapted a graph-based approach for similarity-based partitioning of whole genome 454 sequence reads in order to build clusters made of the reads derived from individual repeat families. The information about cluster sizes was utilized for assessing the proportion and composition of repeats in the genomes of two model species,differing in genome size and 454 sequencing coverage. Moreover, statistical analysis and visual inspection of the topology of the cluster graphs using a newly developed program tool, SeqGrapheR, were shown to be helpful in distinguishing basic types of repeats and investigating sequence variability within repeat families. Repetitive regions of plant genomes can be efficiently characterized by the presented graph-based analysis and the graph representation of repeats can be further used to assess the variability and evolutionary divergence of repeat families, discover and characterize novel elements, and aid in subsequent assembly of their consensus sequences
Pracoviště	Biologické centrum (od r. 2006)
Kontakt	Dana Hypšová, eje@eje.cz, Tel.: 387 775 214
Rok sběru	2011

Počet záznamů: 1