Search results for "peli"
showing 10 items of 1060 documents
A new parallel pipeline for DNA methylation analysis of long reads datasets
2017
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…
Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM
2019
Single-cell transcriptomic assays have enabled the de novo reconstruction of lineage differentiation trajectories, along with the characterization of cellular heterogeneity and state transitions. Several methods have been developed for reconstructing developmental trajectories from single-cell transcriptomic data, but efforts on analyzing single-cell epigenomic data and on trajectory visualization remain limited. Here we present STREAM, an interactive pipeline capable of disentangling and visualizing complex branching trajectories from both single-cell transcriptomic and epigenomic data. We have tested STREAM on several synthetic and real datasets generated with different single-cell techno…
Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus
2016
Background: ChIP-nexus, an extension of the ChIP-exo protocol, can be used to map the borders of protein-bound DNA sequences at nucleotide resolution, requires less input DNA and enables selective PCR duplicate removal using random barcodes. However, the use of random barcodes requires additional preprocessing of the mapping data, which complicates the computational analysis. To date, only a very limited number of software packages are available for the analysis of ChIP-exo data, which have not yet been systematically tested and compared on ChIP-nexus data. Results: Here, we present a comprehensive software package for ChIP-nexus data that exploits the random barcodes for selective removal …
The marine activities performed within the TOMO-ETNA experiment
2016
<p>The TOMO-ETNA experiment was planned in order to obtain a detailed geological and structural model of the continental and oceanic crust beneath Mt. Etna volcano and northeastern Sicily up to the Aeolian Islands (southern Italy), by integrating data from active and passive refraction and reflection seismic methodologies, magnetic and gravity surveys. This paper focuses on the marine activities performed within the experiment, which have been carried out in the Ionian and Tyrrhenian Seas, during three multidisciplinary oceanographic cruises, involving three research vessels (“Sarmiento de Gamboa”, “Galatea” and “Aegaeo”) belonging to different countries and institutions. During the o…
panISa: ab initio detection of insertion sequences in bacterial genomes from short read sequence data.
2018
Abstract Motivation The advent of next-generation sequencing has boosted the analysis of bacterial genome evolution. Insertion sequence (IS) elements play a key role in prokaryotic genome organization and evolution, but their repetitions in genomes complicate their detection from short-read data. Results PanISa is a software pipeline that identifies IS insertions ab initio in bacterial genomes from short-read data. It is a highly sensitive and precise tool based on the detection of read-mapping patterns at the insertion site. PanISa performs better than existing IS detection systems as it is based on a database-free approach. We applied it to a high-risk clone lineage of the pathogenic spec…
Holistic Optimization of Bioinformatic Analysis Pipeline for Detection and Quantification of 2′-O-Methylations in RNA by RiboMethSeq
2020
International audience; A major trend in the epitranscriptomics field over the last 5 years has been the high-throughput analysis of RNA modifications by a combination of specific chemical treatment(s), followed by library preparation and deep sequencing. Multiple protocols have been described for several important RNA modifications, such as 5-methylcytosine (m5C), pseudouridine (ψ), 1-methyladenosine (m1A), and 2'-O-methylation (Nm). One commonly used method is the alkaline cleavage-based RiboMethSeq protocol, where positions of reads' 5'-ends are used to distinguish nucleotides protected by ribose methylation. This method was successfully applied to detect and quantify Nm residues in vari…
Numerical Study on the Heading Misalignment and Current Velocity Reduction of a Vessel-Shaped Offshore Fish Farm
2019
Recently, the concept of a vessel-shaped fish farm was proposed for open sea applications. The fish farm comprises a vessel-shaped floater, five fish cages, and a single-point mooring system. Such a system weathervanes, and this feature increases the spread area of fish waste. Still, the downstream cages may experience decreased exchange of water flow when the vessel heading is aligned with the current direction, and fish welfare may be jeopardized. To ameliorate the flow conditions, a dynamic positioning (DP) system may be required, and its power consumption should relate to the heading misalignment. This paper proposes an integrated method for predicting the heading misalignment between t…
Why Digital Games Can Be Advantageous in Vocabulary Learning
2021
Vocabulary learning is an integral part of language learning; however, it is difficult. Although there are many techniques proposed for vocabulary learning and teaching, researchers still strive to find effective methods. Recently, digital games have shown potentials in enhancing vocabulary acquisition. A majority of studies in digital game-based vocabulary learning (DGBVL) literature investigate the effectiveness of DGBVL tasks. In other words, there are enough answers to what questions in DGBVL literature whereas why questions are rarely answered. Finding such answers help us learn more about the structure of the DGBVL tasks and their effects on vocabulary learning. Hence, to achieve this…
Using UAV Based 3D Modelling to Provide Smart Monitoring of Road Pavement Conditions
2020
Road pavements need adequate maintenance to ensure that their conditions are kept in a good state throughout their lifespans. For this to be possible, authorities need efficient and effective databases in place, which have up to date and relevant road condition information. However, obtaining this information can be very difficult and costly and for smart city applications, it is vital. Currently, many authorities make maintenance decisions by assuming road conditions, which leads to poor maintenance plans and strategies. This study explores a pathway to obtain key information on a roadway utilizing drone imagery to replicate the roadway as a 3D model. The study validates this by using stru…
Semi-automated annotation of page-based documents within the Genre and Multimodality framework
2016
This paper describes ongoing work on a tool developed for annotating document images for their multimodal features and compiling this information into a corpus. The tool leverages open source computer vision and natural language processing libraries to describe the content and structure of multimodal documents and to generate multiple layers of XML annotation. The paper introduces the annotation schema, describes the document processing pipeline and concludes with a brief description of future work.