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Representing GC variation along eukaryotic chromosomes
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SYSNO ASEP 0105339 Druh ASEP J - Článek v odborném periodiku Zařazení RIV J - Článek v odborném periodiku Poddruh J Ostatní články Název Representing GC variation along eukaryotic chromosomes Překlad názvu Zobrazení variace GC v eukaryotických chromozomech Tvůrce(i) Pačes, Jan (UMG-J) RID, ORCID
Zíka, Radek (UMG-J)
Pačes, Václav (UMG-J) RID
Pavlíček, A. (US)
Clay, O. (IT)
Bernardi, G. (IT)Zdroj.dok. Gene. - : Elsevier - ISSN 0378-1119
Roč. 333, - (2004), s. 135-141Poč.str. 7 s. Jazyk dok. eng - angličtina Země vyd. NL - Nizozemsko Klíč. slova GC content ; genome organization ; compositional homogenity Vědní obor RIV EB - Genetika a molekulární biologie CEP LN00A079 GA MŠMT - Ministerstvo školství, mládeže a tělovýchovy CEZ AV0Z5052915 - UMG-J Anotace Genome sequencing now permits direct visual representation, at any scale, of GC heterogeneity along the chromosomes of several higher eukaryotes. Plots can be easily obtained from the chromosomal sequences, yet sequence releases of mammalian or plant chromosomes still tend to use small scales or window sizes that obscure important large-scale compositional features. To faithfully reveal, at one glance, the compositional variation at a given scale, we have devised a simple scheme that combines line plots with color-coded shading of the regions underneath the plots. The scheme can be applied to different eukaryotic genomes to facilitate their comparison, as illustrated here for a sample of chromosomes chosen from seven selected species. As a complement to a previously published compact view of isochores in the human genome sequence [FEBS Lett. 511 (2002a) 165], we include here an analogous map for the recently sequenced mouse genome, and discuss the contribution of repetitive DNA to the GC variation along the plots. Supplementary information, including a database of color-coded GC profiles for all recently sequenced eukaryotes and the program draw_chromosomes_gc.pl used to obtain them, are available at http://genomat.img.cas.cz Pracoviště Ústav molekulární genetiky Kontakt Nikol Škňouřilová, nikol.sknourilova@img.cas.cz, Tel.: 241 063 217 Rok sběru 2010
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