2014
Uneven distribution of potential triplex sequences in the human genome. In silico study using the R/Bioconductor package triplex.
LEXA, Matej, Tomáš MARTÍNEK a Marie BRÁZDOVÁZákladní údaje
Originální název
Uneven distribution of potential triplex sequences in the human genome. In silico study using the R/Bioconductor package triplex.
Autoři
LEXA, Matej (703 Slovensko, garant, domácí), Tomáš MARTÍNEK (203 Česká republika) a Marie BRÁZDOVÁ (203 Česká republika)
Vydání
Angers, France, Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, od s. 80-88, 9 s. 2014
Nakladatel
SciTePress
Další údaje
Jazyk
angličtina
Typ výsledku
Stať ve sborníku
Obor
10201 Computer sciences, information science, bioinformatics
Stát vydavatele
Francie
Utajení
není předmětem státního či obchodního tajemství
Forma vydání
tištěná verze "print"
Odkazy
Kód RIV
RIV/00216224:14330/14:00074890
Organizační jednotka
Fakulta informatiky
ISBN
978-989-758-012-3
Klíčová slova anglicky
Human genome; DNA sequence; Non-B-DNA; Triplex; Bioconductor; Repetitive sequences; Mobile DNA; Lexicographically minimal rotation
Příznaky
Mezinárodní význam, Recenzováno
Změněno: 27. 4. 2015 21:44, RNDr. Pavel Šmerk, Ph.D.
Anotace
V originále
Eukaryotic genomes are rich in sequences capable of forming non-B DNA structures. These structures are expected to play important roles in natural regulatory processes at levels above those of individual genes, such as whole genome dynamics or chromatin organization, as well as in processes leading to the loss of these functions, such as cancer development. Recently, a number of authors have mapped the occurrence of potential quadruplex sequences in the human genome and found them to be associated with promoters. In this paper, we set out to map the distribution and characteristics of potential triplex-forming sequences in human genome DNA sequences. Using the R/Bioconductor package {\it triplex}, we found these sequences to be excluded from exons, while present mostly in a small number of repetitive sequence classes, especially short sequence tandem repeats (microsatellites), Alu and combined elements, such as SVA. We also introduce a novel way of classifying potential triplex sequences, using a lexicographically minimal rotation of the most frequent k-mer to assign class membership automatically. Members of such classes typically have different propensities to form parallel and antiparallel intramolecular triplexes (H-DNA). We observed an interesting pattern, where the predicted third strands of antiparallel H-DNA were much less likely to contain a deletion against their duplex structural counterpart than were their parallel versions.
Návaznosti
EE2.3.20.0189, projekt VaV |
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