0000000000480365
AUTHOR
Javier Chaves
HPG-HMapper: A DNA hydroxymethylation analysis tool
DNA methylation (mC) and hydroxymethylation (hmC) can significantly affect the normal human development, as well as health and disease status. hmC studies require not only specific treatment of DNA, but also software tools for their analysis. However, there are no software tools capable of analyzing DNA hmC currently. In this article, we propose HPG-HMapper, a parallel software tool for analyzing the DNA hmC data obtained by ten-eleven translocation–assisted bisulfite sequencing. This tool takes as input data the output files of mC aligner tools, and it yields mC maps and the accounting of methylated and hydroxymethylated bases on each chromosome. The design of this tool includes the consi…
Zinc and smoking habits in the setting of hypertension in a Spanish populations.
The objective of this study was to evaluate the relationship between trace and toxic amounts of zinc (Zn) in biological samples (blood and urine) and the smoking habits of hypertensive patients and healthy control subjects in Valladolid (Spain). In order to compare biological samples, the concentrations of these samples were measured using inductively coupled plasma mass spectrometry. The limits of detection for Zn in blood plasma ranged between 4.22 and 17.34 μmol l(-1) and were <0.08 μmol g(-1) creatinine in urine. The results of this study indicate that the highest mean values of serum Zn were found in non-hypertensive nonsmokers (13.39±4.35 μmol l(-1)), whereas the highest urine Zn valu…
On the Use of Binary Trees for DNA Hydroxymethylation Analysis
DNA methylation (mC) and hydroxymethylation (hmC) can have a significant effect on normal human development, health and disease status. Hydroxymethylation studies require specific treatment of DNA, as well as software tools for their analysis. In this paper, we propose a parallel software tool for analyzing the DNA hydroxymethylation data obtained by TAB-seq. The software is based on the use of binary trees for searching the different occurrences of methylation and hydroxymethylation in DNA samples. The binary trees allow to efficiently store and access the information about the methylation of each methylated/hydroxymethylated cytosines in the samples. Evaluation results shows that the perf…