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Sequence alignment is a core step in the processing of DNA and RNA sequencing data. In this paper, we present a high performance GPU accelerated set of APIs (GASAL) for pairwise sequence alignment of DNA and RNA sequences. The GASAL APIs provide accelerated kernels for local, global as well as semi-global alignment, allowing the computation of the alignment score, and optionally the start and end...
Next-generation sequencing (NGS) is becoming feasible for identification or diagnosis of human infectious diseases. In the present study, we aimed to develop a bioinformatic method for dengue virus identification by comparison against different database for variant types of samples and BLASTn and ViPR databases. We collected 12 different types of samples from five dengue-virus-infected patients and...
Nowadays, Next Generation Sequeencing (NGS) is a catch-all term used to describe different modern DNA sequencing applications that produce big genomics data that can be analysed in a faster fashion than in the past. For this reason, NGS requires more and more sophisticated algorithms and high-performance parallel processing systems able to analyse and extract knowledge from a huge amount of genomics...
The adoption of Big Data technologies can potentially boost the scalability of data-driven biology and health workflows by orders of magnitude. Consider, for instance, that technologies in the Hadoop ecosystem have been successfully used in data-driven industry to scale their processes to levels much larger than any biological-or health-driven work attempted thus far. In this work we demonstrate the...
The advent of Cloud computing is changing the way of conceiving information and communication systems in different application fields including Biotechnology. In this context, an emerging research field is Next-Generation Sequencing (NGS) that includes several recent technologies allowing sequencing DNA and that have revolutionized the study of genomics and molecular biology. These cutting-edge sequencing...
Continuous improvements on Next-Generation Sequencing approaches are providing a wealth of data for life sciences, and massive application of ICT (Information and Communication Technologies) to molecular research has become essential for the progress of medical research. While several software tools have been developed to assist in analysis, there is still a lack of a focused and integrated solution...
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