Počet záznamů: 1
Global sequence characterization of rice centromeric satellite based on oligomer frequency analysis in large-scale sequencing data
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SYSNO ASEP 0348727 Druh ASEP J - Článek v odborném periodiku Zařazení RIV J - Článek v odborném periodiku Poddruh J Článek ve WOS Název Global sequence characterization of rice centromeric satellite based on oligomer frequency analysis in large-scale sequencing data Tvůrce(i) Macas, Jiří (BC-A) RID, ORCID, SAI
Neumann, Pavel (BC-A) RID, ORCID
Novák, Petr (BC-A) RID, ORCID
Jiang, J. (US)Celkový počet autorů 4 Zdroj.dok. Bioinformatics. - : Oxford University Press - ISSN 1367-4803
Roč. 26, č. 1797 (2010), s. 2101-2108Poč.str. 8 s. Jazyk dok. eng - angličtina Země vyd. GB - Velká Británie Klíč. slova next-generation sequencing ; satellite repeats ; K-mer analysis Vědní obor RIV EB - Genetika a molekulární biologie CEP KJB500960802 GA AV ČR - Akademie věd 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 000281738900005 DOI 10.1093/bioinformatics/btq343 Anotace K-mer frequency spectra were determined for two sets of rice centromeric satellite CentO sequences, including 454 reads from ChIP-sequencing of CENH3-bound DNA (7.6 Mb) and the whole genome Sanger sequencing reads (5.8 Mb). K-mer frequencies were used to identify the most conserved sequence regions and to reconstruct consensus sequences of complete monomers. Reconstructed consensus sequences as well as the assessment of overall divergence of k-mer spectra revealed high similarity of the two datasets, suggesting that CentO sequences associated with functional centromeres do not significantly differ from the total population of CentO, which includes both centromeric and pericentromeric repeat arrays. On the other hand, considerable differences were revealed when these methods were used for comparison of CentO populations between individual chromosomes of the rice genome assembly, demonstrating preferential sequence homogenization of the clusters within the same chromosome. Pracoviště Biologické centrum (od r. 2006) Kontakt Dana Hypšová, eje@eje.cz, Tel.: 387 775 214 Rok sběru 2011
Počet záznamů: 1