A parallel and sensitive software tool for methylation analysis on multicore platforms.

Abstract Motivation: DNA methylation analysis suffers from very long processing time, as the advent of Next-Generation Sequencers has shifted the bottleneck of genomic studies from the sequencers that obtain the DNA samples to the software that performs the analysis of these samples. The existing software for methylation analysis does not seem to scale efficiently neither with the size of the dataset nor with the length of the reads to be analyzed. As it is expected that the sequencers will provide longer and longer reads in the near future, efficient and scalable methylation software should be developed. Results: We present a new software tool, called HPG-Methyl, which efficiently maps bis…

Virtual reality for driving simulation

In this paper, the authors describe the data structure necessary to provide real time simulation and visualization of complex environments and situations. Through the SIRCA project, the development of driving oriented simulators, using Virtual Reality (VR) and evaluating it in comparison with convention technologies, has taken place. Focus is on some of the algorithms and data structure required to provide real time simulation of the complex urban environment and its visualization under the conditions of VR devices.

Non-interleaved Quadtree Node Codification

The usual quadtree node non-pointer codification is based on interleaved binary representations of node coordinates, in such a way that every operation that concerns to the spatial position or to the specific orientation of the region represented by the node needs to undo this interleaving process. So, the computation time of such operations is linear with the node depth. In this paper an alternative codification is presented called “non-interleaved codification”. The new codification has a simpler management and a higher intuitiveness than current codifications that use the interleaving approach. The proposed codification is more efficient than previous ones for the following set of operat…

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…

Terrain data compression using wavelet-tiled pyramids for online 3D terrain visualization

Last years have witnessed the widespread use of online terrain visualization applications. However, the significant improvements achieved in sensing technologies have allowed an increasing size of the terrain databases. These increasing sizes represent a serious drawback when terrain data must be transmitted and rendered at interactive rates. In this paper, we propose a novel wavelet-tiled pyramid for compressing terrain data that replaces the traditional multiresolution pyramid usually used in wavelet compression schemes. The new wavelet-tiled pyramid modifies the wavelet analysis and synthesis processes, allowing an efficient transmission and reconstruction of terrain data in those applic…

Efficient Coding of Quadtree Nodes

In this paper an alternative non-pointer quadtree node codification to manage geographical spatial data is presented. New codification is based on a variable sequence of z-ordered base four digits. Memory requirements of the new codification are lower than previous codifications, and in particular lower than FD codification, the most commonly used in linear quadtrees. Furthermore, z-ordering makes compatible new codification with most of the algorithms developed for FD.

A new approach for the visualization of DNA methylation results

Locally constrained synthetic LoDs generation for natural terrain meshes

Terrain representation is a basic topic in the field of interactive graphics. The amount of data required for a good quality of the terrain offers an important challenge to developers of such systems. For users of these applications, the accuracy of geographical data is generally less important than its natural visual appearance. This makes it possible to maintain a limited geographical database for the system and to extend it generating synthetic data. The evaluation of the intrinsic properties of the terrain (i.e. fractal dimension, roughness, etc.) may be used as the basis for generating extra data accomplishing the same patterns discovered in the actual information. However, it is also …

Hybrid P2P schemes for remote terrain interactive visualization systems

Over the last few years, there has been a lot of development of interactive terrain visualization applications using remote databases. One of the main problems that these applications must face is scalability. These applications usually use a client-server model that cannot support a large number of concurrent requests without using a considerable number of servers. In this paper, we present a full comparative study of new hybrid P2P schemes for terrain interactive visualization systems. The performance evaluation results show that the best strategy consists of avoiding the periodical reporting among peer nodes about the current information contained in each node, while using some servers a…

A new parallel pipeline for DNA methylation analysis of long reads datasets

Background DNA methylation is an important mechanism of epigenetic regulation in development and disease. New generation sequencers allow genome-wide measurements of the methylation status by reading short stretches of the DNA sequence (Methyl-seq). Several software tools for methylation analysis have been proposed over recent years. However, the current trend is that the new sequencers and the ones expected for an upcoming future yield sequences of increasing length, making these software tools inefficient and obsolete. Results In this paper, we propose a new software based on a strategy for methylation analysis of Methyl-seq sequencing data that requires much shorter execution times while…

Visualization of Large Terrain Using Non-restricted Quadtree Triangulations

This paper presents a set of new techniques oriented towards the real-time visualization of large terrains. These techniques are mainly focused on semi-regular triangulations of non-restricted quadtree terrain representations. Despite the fact that the paper shows that triangulations based on non-restricted quadtrees are as simple and efficient as those based on restricted quadtrees, the new triangulations avoid discontinuity problems among the boundaries of different patches without the need for tree balancing and extra triangles addition. Another important feature of the proposed triangulation is that it incorporates an efficient method for building triangle strips and triangle fans for t…

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…

Adding Synthetic Detail to Natural Terrain Using a Wavelet Approach

Terrain representation is a basic topic in the field of interactive graphics. The amount of data required for good quality terrain representation offers an important challenge to developers of such systems. For users of these applications the accuracy of geographical data is less important than their natural visual appearance. This makes it possible to mantain a limited geographical data base for the system and to extend it generating synthetic data.In this paper we combine fractal and wavelet theories to provide extra data which keeps the natural essence of actual information available. The new levels of detail(LOD) for the terrain are obtained applying an inverse Wavelet Transform (WT) to…

Additional file 1 of A new parallel pipeline for DNA methylation analysis of long reads datasets

Text document containing an example of the command launched to execute each of the tools. (TXT 2 kb)