17 research outputs found
Assessment of nitrate-N contamination in the Chunnakam aquifer system, Jaffna Peninsula, Sri Lanka
NucTools: analysis of chromatin feature occupancy profiles from high-throughput sequencing data
Background: Biomedical applications of high-throughput sequencing methods generate a vast amount of data in which numerous chromatin features are mapped along the genome. The results are frequently analysed by creating binary data sets that link the presence/absence of a given feature to specific genomic loci. However, the nucleosome occupancy or chromatin accessibility landscape is essentially continuous. It is currently a challenge in the field to cope with continuous distributions of deep sequencing chromatin readouts and to integrate the different types of discrete chromatin features to reveal linkages between them. Results: Here we introduce the NucTools suite of Perl scripts as well as MATLAB- and R-based visualization programs for a nucleosome-centred downstream analysis of deep sequencing data. NucTools accounts for the continuous distribution of nucleosome occupancy. It allows calculations of nucleosome occupancy profiles averaged over several replicates, comparisons of nucleosome occupancy landscapes between different experimental conditions, and the estimation of the changes of integral chromatin properties such as the nucleosome repeat length. Furthermore, NucTools facilitates the annotation of nucleosome occupancy with other chromatin features like binding of transcription factors or architectural proteins, and epigenetic marks like histone modifications or DNA methylation. The applications of NucTools are demonstrated for the comparison of several datasets for nucleosome occupancy in mouse embryonic stem cells (ESCs) and mouse embryonic fibroblasts (MEFs). Conclusions: The typical workflows of data processing and integrative analysis with NucTools reveal information on the interplay of nucleosome positioning with other features such as for example binding of a transcription factor CTCF, regions with stable and unstable nucleosomes, and domains of large organized chromatin K9me2 modifications (LOCKs). As potential limitations and problems we discuss how inter-replicate variability of MNase-seq experiments can be addressed
Assessment of groundwater quality and groundwater vulnerability in the northern Ordos Cretaceous Basin, China
Application of DRASTIC model and GIS for evaluation of aquifer vulnerability: case study of Asadabad, Hamadan (western Iran)
Assessing the vulnerability of groundwater due to open pit coal mining using DRASTIC model: a case study of Phulbari Coal Mine, Bangladesh
Multi-criteria potential groundwater contamination and human activities: Araras watershed, Brazil
Gold nanoparticle assemblies stabilized by bis(phthalocyaninato)lanthanide(III) complexes through van der Waals interactions
Groundwater vulnerability assessment of a coastal aquifer system at River Nestos eastern Delta, Greece
A Comparative Study on the Effect of CNT or Alumina Nanoparticles on the Tensile Properties of Epoxy Nanocomposites
EFFECTIVENESS RISE OF REFRIGERATING PLANTS OF RAILWAY TRANSPORT BY OPTIMIZATION OF THEIR OPERATION MODE
There the procedure of statical and dynamical optimization of refrigerating system on the basis of thermo-economic approach has been developed. The influence of different factors (the temperature of heat sources, the effectiveness of separate members etc.) on the value of optimizing variables has been brought out. The law of optimum control over the refrigerating plant under the different climatic conditions has been obtainedAvailable from VNTIC / VNTIC - Scientific & Technical Information Centre of RussiaSIGLERURussian Federatio